List of RNA-Seq Bioinformatics Tools (509 items)report

Type

Quantity

PROPER : PROspective Power Evaluation for RNAseq. (Design)
RNAtor Android Application to calculate optimal parameters for popular tools and kits available for DNA sequencing projects. (Design)
Scotty : a web tool for designing RNA-Seq experiments to measure differential gene expression. (Design)
ssizeRNA Sample Size Calculation for RNA-Seq Experimental Design. (Design)
AfterQC - Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data.

(Quality control) (Quality control, trimming, error correction and pre-processing of data)
dupRadar An R package which provides functions for plotting and analyzing the duplication rates dependent on the expression levels.

(Quality control) (Quality control, trimming, error correction and pre-processing of data)
FastQC is a quality control tool for high-throughput sequence data (Babraham Institute) and is developed in Java. Import of data is possible from FastQ files, BAM or SAM format. This tool provides an overview to inform about problematic areas, summary graphs and tables to rapid assessment of data. Results are presented in HTML permanent reports. FastQC can be run as a stand-alone application or it can be integrated into a larger pipeline solution.

(Quality control) (Quality control, trimming, error correction and pre-processing of data)
fastqp Simple FASTQ quality assessment using Python.

(Quality control) (Quality control, trimming, error correction and pre-processing of data)
Kraken: A set of tools for quality control and analysis of high-throughput sequence data.

(Quality control) (Quality control, trimming, error correction and pre-processing of data)
HTSeq . The Python script htseq-qa takes a file with sequencing reads (either raw or aligned reads) and produces a PDF file with useful plots to assess the technical quality of a run.

(Quality control) (Quality control, trimming, error correction and pre-processing of data)
mRIN - Assessing mRNA integrity directly from RNA-Seq data.

(Quality control) (Quality control, trimming, error correction and pre-processing of data)
MultiQC - Aggregate and visualise results from numerous tools (FastQC, HTSeq, RSeQC, Tophat, STAR, others..) across all samples into a single report.

(Quality control) (Quality control, trimming, error correction and pre-processing of data)
NGSQC: cross-platform quality analysis pipeline for deep sequencing data.

(Quality control) (Quality control, trimming, error correction and pre-processing of data)
NGS QC Toolkit A toolkit for the quality control (QC) of next generation sequencing (NGS) data. The toolkit comprises user-friendly stand alone tools for quality control of the sequence data generated using Illumina and Roche 454 platforms with detailed results in the form of tables and graphs, and filtering of high-quality sequence data. It also includes few other tools, which are helpful in NGS data quality control and analysis.

(Quality control) (Quality control, trimming, error correction and pre-processing of data)
PRINSEQ is a tool that generates summary statistics of sequence and quality data and that is used to filter, reformat and trim next-generation sequence data. It is particular designed for 454/Roche data, but can also be used for other types of sequence.

(Quality control) (Quality control, trimming, error correction and pre-processing of data)
QC-Chain is a package of quality control tools for next generation sequencing (NGS) data, consisting of both raw reads quality evaluation and de novo contamination screening, which could identify all possible contamination sequences.

(Quality control) (Quality control, trimming, error correction and pre-processing of data)
QC3 a quality control tool designed for DNA sequencing data for raw data, alignment, and variant calling.

(Quality control) (Quality control, trimming, error correction and pre-processing of data)
qrqc Quickly scans reads and gathers statistics on base and quality frequencies, read length, and frequent sequences. Produces graphical output of statistics for use in quality control pipelines, and an optional HTML quality report. S4 SequenceSummary objects allow specific tests and functionality to be written around the data collected.

(Quality control) (Quality control, trimming, error correction and pre-processing of data)
RNA-SeQC is a tool with application in experiment design, process optimization and quality control before computational analysis. Essentially, provides three types of quality control: read counts (such as duplicate reads, mapped reads and mapped unique reads, rRNA reads, transcript-annotated reads, strand specificity), coverage (like mean coverage, mean coefficient of variation, 5’/3’ coverage, gaps in coverage, GC bias) and expression correlation (the tool provides RPKM-based estimation of expression levels). RNA-SeQC is implemented in Java and is not required installation, however can be run using the GenePattern web interface. The input could be one or more BAM files. HTML reports are generated as output.

(Quality control) (Quality control, trimming, error correction and pre-processing of data)
RSeQC analyzes diverse aspects of RNA-Seq experiments: sequence quality, sequencing depth, strand specificity, GC bias, read distribution over the genome structure and coverage uniformity. The input can be SAM, BAM, FASTA, BED files or Chromosome size file (two-column, plain text file). Visualization can be performed by genome browsers like UCSC, IGB and IGV. However, R scripts can also be used to visualization.

(Quality control) (Quality control, trimming, error correction and pre-processing of data)
SAMStat identifies problems and reports several statistics at different phases of the process. This tool evaluates unmapped, poorly and accurately mapped sequences independently to infer possible causes of poor mapping.

(Quality control) (Quality control, trimming, error correction and pre-processing of data)
SolexaQA calculates sequence quality statistics and creates visual representations of data quality for second-generation sequencing data. Originally developed for the Illumina system (historically known as “Solexa”), SolexaQA now also supports Ion Torrent and 454 data.

(Quality control) (Quality control, trimming, error correction and pre-processing of data)
Trim galore is a wrapper script to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files (for directional, non-directional (or paired-end) sequencing).

(Quality control) (Quality control, trimming, error correction and pre-processing of data)
BBDuk Ultrafast, multithreaded tool to trim adapters and filter or mask contaminants based on kmer-matching, allowing a hamming- or edit-distance, as well as degenerate bases. Also performs optimal quality-trimming and filtering, format conversion, contaminant concentration reporting, gc-filtering, length-filtering, entropy-filtering, chastity-filtering, and generates text histograms for most operations. Interconverts between fastq, fasta, sam, scarf, interleaved and 2-file paired, gzipped, bzipped, ASCII-33 and ASCII-64. Keeps pairs together. Open-source, written in pure Java; supports all platforms with no recompilation and no other dependencies.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
clean_reads cleans NGS (Sanger, 454, Illumina and solid) reads. It can trim bad quality regions, adaptors, vectors, and regular expressions. It also filters out the reads that do not meet a minimum quality criteria based on the sequence length and the mean quality.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
condetri is a method for content dependent read trimming for Illumina data using quality scores of each base individually. It is independent from sequencing coverage and user interaction. The main focus of the implementation is on usability and to incorporate read trimming in next-generation sequencing data processing and analysis pipelines. It can process single-end and paired-end sequencing data of arbitrary length.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
cutadapt removes adapter sequences from next-generation sequencing data (Illumina, SOLiD and 454). It is used especially when the read length of the sequencing machine is longer than the sequenced molecule, like the microRNA case.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
Deconseq Detect and remove contaminations from sequence data.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
Erne-Filter is a short string alignment package whose goal is to provide an all-inclusive set of tools to handle short (NGS-like) reads. ERNE comprises ERNE-FILTER (read trimming and continamination filtering), ERNE-MAP (core alignment tool/algorithm), ERNE-BS5 (bisulfite treated reads aligner), and ERNE-PMAP/ERNE-PBS5 (distributed versions of the aligners).

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
FastqMcf Fastq-mcf attempts to: Detect & remove sequencing adapters and primers; Detect limited skewing at the ends of reads and clip; Detect poor quality at the ends of reads and clip; Detect Ns, and remove from ends; Remove reads with CASAVA 'Y' flag (purity filtering); Discard sequences that are too short after all of the above; Keep multiple mate-reads in sync while doing all of the above.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
FASTX Toolkit is a set of command line tools to manipulate reads in files FASTA or FASTQ format. These commands make possible preprocess the files before mapping with tools like Bowtie. Some of the tasks allowed are: conversion from FASTQ to FASTA format, information about statistics of quality, removing sequencing adapters, filtering and cutting sequences based on quality or conversion DNA/RNA.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
Flexbar performs removal of adapter sequences, trimming and filtering features.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
FreClu improves overall alignment accuracy performing sequencing-error correction by trimming short reads, based on a clustering methodology.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
htSeqTools is a Bioconductor package able to perform quality control, processing of data and visualization. htSeqTools makes possible visualize sample correlations, to remove over-amplification artifacts, to assess enrichment efficiency, to correct strand bias and visualize hits.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
NxTrim Adapter trimming and virtual library creation routine for Illumina Nextera Mate Pair libraries.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
PRINSEQ generates statistics of your sequence data for sequence length, GC content, quality scores, n-plicates, complexity, tag sequences, poly-A/T tails, odds ratios. Filter the data, reformat and trim sequences.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
Sabre A barcode demultiplexing and trimming tool for FastQ files.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
Scythe A 3'-end adapter contaminant trimmer.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
SEECER is a sequencing error correction algorithm for RNA-seq data sets. It takes the raw read sequences produced by a next generation sequencing platform like machines from Illumina or Roche. SEECER removes mismatch and indel errors from the raw reads and significantly improves downstream analysis of the data. Especially if the RNA-Seq data is used to produce a de novo transcriptome assembly, running SEECER can have tremendous impact on the quality of the assembly.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
Sickle A windowed adaptive trimming tool for FASTQ files using quality.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
SnoWhite is a pipeline designed to flexibly and aggressively clean sequence reads (gDNA or cDNA) prior to assembly. It takes in and returns fastq or fasta formatted sequence files.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
ShortRead is a package provided in the R (programming language) / BioConductor environments and allows input, manipulation, quality assessment and output of next-generation sequencing data. This tool makes possible manipulation of data, such as filter solutions to remove reads based on predefined criteria. ShortRead could be complemented with several Bioconductor packages to further analysis and visualization solutions (BioStrings, BSgenome, IRanges, and so on).

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
SortMeRNA is a program tool for filtering, mapping and OTU-picking NGS reads in metatranscriptomic and metagenomic data. The core algorithm is based on approximate seeds and allows for fast and sensitive analyses of nucleotide sequences. The main application of SortMeRNA is filtering ribosomal RNA from metatranscriptomic data.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
TagCleaner The TagCleaner tool can be used to automatically detect and efficiently remove tag sequences (e.g. WTA tags) from genomic and metagenomic datasets. It is easily configurable and provides a user-friendly interface.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
Trimmomatic performs trimming for Illumina platforms and works with FASTQ reads (single or pair-ended). Some of the tasks executed are: cut adapters, cut bases in optional positions based on quality thresholds, cut reads to a specific length, converts quality scores to Phred-33/64.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
fastp A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
FASTX-Toolkit The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
UCHIME is an algorithm for detecting chimeric sequences.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
ChimeraSlayer is a chimeric sequence detection utility, compatible with near-full length Sanger sequences and shorter 454-FLX sequences (~500 bp).

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
Acacia Error-corrector for pyrosequenced amplicon reads.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
AllPathsLG error correction.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
AmpliconNoise AmpliconNoise is a collection of programs for the removal of noise from 454 sequenced PCR amplicons. It involves two steps the removal of noise from the sequencing itself and the removal of PCR point errors. This project also includes the Perseus algorithm for chimera removal.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
BayesHammer. Bayesian clustering for error correction. This algorithm is based on Hamming graphs and Bayesian subclustering. While BAYES HAMMER was designed for single-cell sequencing, it also improves on existing error correction tools for bulk sequencing data.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
Bless A bloom filter-based error correction solution for high-throughput sequencing reads.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
Blue Blue is a short-read error-correction tool based on k-mer consensus and context.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
bf A sequencing error corrector designed for Illumina short reads. It uses a non-greedy algorithm with a speed comparable to implementations based on greedy methods.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
Denoiser Denoiser is designed to address issues of noise in pyrosequencing data. Denoiser is a heuristic variant of PyroNoise. Developers of denoiser report a good agreement with PyroNoise on several test datasets.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
Echo A reference-free short-read error correction algorithm.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
Lighter. A fast and memory-efficient sequencing error correction without counting.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
LSC LSC uses short Illumina reads to corrected errors in long reads.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
Karect Karect: accurate correction of substitution, insertion and deletion errors for next-generation sequencing data.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
NoDe NoDe: a fast error-correction algorithm for pyrosequencing amplicon reads.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
PyroTagger PyroTagger: A fast, accurate pipeline for analysis of rRNA amplicon pyrosequence data.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
Quake is a tool to correct substitution sequencing errors in experiments with deep coverage for Illumina sequencing reads.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
QuorUM: An Error Corrector for Illumina Reads.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
Rcorrector. Error correction for Illumina RNA-seq reads.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
Reptile is a software developed in C++ for correcting sequencing errors in short reads from next-gen sequencing platforms.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
Seecer SEquencing Error CorrEction for Rna reads.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
SGA.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
SOAP denovo.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
UNOISE.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
Alpine Modeling and correcting fragment sequence bias for RNA-seq.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
cqn is a normalization tool for RNA-Seq data, implementing the conditional quantile normalization method.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
EDASeq is a Bioconductor package to perform GC-Content Normalization for RNA-Seq Data.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
GeneScissors A comprehensive approach to detecting and correcting spurious transcriptome inference due to RNAseq reads misalignment.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
Peer is a collection of Bayesian approaches to infer hidden determinants and their effects from gene expression profiles using factor analysis methods. Applications of PEER have: a) detected batch effects and experimental confounders, b) increased the number of expression QTL findings by threefold, c) allowed inference of intermediate cellular traits, such as transcription factor or pathway activations.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
RUV is a R package that implements the remove unwanted variation (RUV) methods of Risso et al. (2014) for the normalization of RNA-Seq read counts between samples.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
svaSurrogate Variable Analysis.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
svaseq removing batch effects and other unwanted noise from sequencing data.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
SysCall is a classifier tool to identification and correction of systematic error in high-throughput sequence data.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
AuPairWise A Method to Estimate RNA-Seq Replicability through Co-expression.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
BamHash is a checksum based method to ensure that the read pairs in FASTQ files match exactly the read pairs stored in BAM files, regardless of the ordering of reads. BamHash can be used to verify the integrity of the files stored and discover any discrepancies. Thus, BamHash can be used to determine if it is safe to delete the FASTQ files storing raw sequencing reads after alignment, without the loss of data.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
BBMerge Merges paired reads based on overlap to create longer reads, and an insert-size histogram. Fast, multithreaded, and yields extremely few false positives. Open-source, written in pure Java; supports all platforms with no recompilation and no other dependencies. Distributed with BBMap.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
Biopieces are a collection of bioinformatics tools that can be pieced together in a very easy and flexible manner to perform both simple and complex tasks. The Biopieces work on a data stream in such a way that the data stream can be passed through several different Biopieces, each performing one specific task: modifying or adding records to the data stream, creating plots, or uploading data to databases and web services.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
COPE COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
DeconRNASeq is an R package for deconvolution of heterogeneous tissues based on mRNA-Seq data.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
FastQ Screen screens FASTQ format sequences to a set of databases to confirm that the sequences contain what is expected (such as species content, adapters, vectors, etc.).

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
FLASH is a read pre-processing tool. FLASH combines paired-end reads which overlap and converts them to single long reads.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
IDCheck

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
ORNA and ORNA Q/K A tool for reducing redundancy in RNA-seq data which reduces the computational resource requirements of an assembler

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
PANDASeq.is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
PEAR PEAR: A fast and accurate Illumina Paired-End reAd mergeR.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
qRNASeq script The qRNAseq tool can be used to accurately eliminate PCR duplicates from RNA-Seq data if Molecular Indexes™ or other stochastic labels have been used during library prep.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
SHERA a SHortread Error-Reducing Aligner.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
XORRO Rapid Paired-End Read Overlapper.

(Improving the quality) (Quality control, trimming, error correction and pre-processing of data)
BFAST aligns short reads to reference sequences and presents particular sensitivity towards errors, SNPs, insertions and deletions. BFAST works with the Smith-Waterman algorithm. See also seqanwers/BFAST.

(Short (unspliced) aligners) (Alignment tools)
Bowtie is a fast short aligner using an algorithm based on the Burrows-Wheeler transform and the FM-index. Bowtie tolerates a small number of mismatches.

(Short (unspliced) aligners) (Alignment tools)
Bowtie2 Bowtie 2 is a memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly recommended for aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.

(Short (unspliced) aligners) (Alignment tools)
Burrows-Wheeler Aligner (BWA) BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is designed for Illumina sequence reads up to 100bp, while the rest two for longer sequences ranged from 70bp to 1Mbp. BWA-MEM and BWA-SW share similar features such as long-read support and split alignment, but BWA-MEM, which is the latest, is generally recommended for high-quality queries as it is faster and more accurate. BWA-MEM also has better performance than BWA-backtrack for 70-100bp Illumina reads.

(Short (unspliced) aligners) (Alignment tools)
Short Oligonucleotide Analysis Package (SOAP)

(Short (unspliced) aligners) (Alignment tools)
GNUMAP performs alignment using a probabilistic Needleman-Wunsch algorithm. This tool is able to handle alignment in repetitive regions of a genome without losing information. The output of the program was developed to make possible easy visualization using available software.

(Short (unspliced) aligners) (Alignment tools)
Maq first aligns reads to reference sequences and after performs a consensus stage. On the first stage performs only ungapped alignment and tolerates up to 3 mismatches.

(Short (unspliced) aligners) (Alignment tools)
Mosaik Mosaik is able to align reads containing short gaps using Smith-Waterman algorithm, ideal to overcome SNPs, insertions and deletions.

(Short (unspliced) aligners) (Alignment tools)
NovoAlign (commercial) is a short aligner to the Illumina platform based on Needleman-Wunsch algorithm. It is able to deal with bisulphite data. Output in SAM format.

(Short (unspliced) aligners) (Alignment tools)
PerM is a software package which was designed to perform highly efficient genome scale alignments for hundreds of millions of short reads produced by the ABI SOLiD and Illumina sequencing platforms. PerM is capable of providing full sensitivity for alignments within 4 mismatches for 50bp SOLID reads and 9 mismatches for 100bp Illumina reads.

(Short (unspliced) aligners) (Alignment tools)
RazerS

(Short (unspliced) aligners) (Alignment tools)
SEAL uses a MapReduce model to produce distributed computing on clusters of computers. Seal uses BWA to perform alignment and Picard MarkDuplicates to detection and duplicate read removal.

(Short (unspliced) aligners) (Alignment tools)
segemehl

(Short (unspliced) aligners) (Alignment tools)
SeqMap

(Short (unspliced) aligners) (Alignment tools)
SHRiMP employs two techniques to align short reads. Firstly, the q-gram filtering technique based on multiple seeds identifies candidate regions. Secondly, these regions are investigated in detail using Smith-Waterman algorithm.

(Short (unspliced) aligners) (Alignment tools)
SMALT

(Short (unspliced) aligners) (Alignment tools)
Stampy combines the sensitivity of hash tables and the speed of BWA. Stampy is prepared to alignment of reads containing sequence variation like insertions and deletions. It is able to deal with reads up to 4500 bases and presents the output in SAM format.

(Short (unspliced) aligners) (Alignment tools)
Subread is a read aligner. It uses the seed-and-vote mapping paradigm to determine the mapping location of the read by using its largest mappable region. It automatically decides whether the read should be globally mapped or locally mapped. For RNA-seq data, Subread should be used for the purpose of expression analysis. Subread can also be used to map DNA-seq reads.

(Short (unspliced) aligners) (Alignment tools)
ZOOM (commercial) is a short aligner of the Illumina/Solexa 1G platform. ZOOM uses extended spaced seeds methodology building hash tables for the reads, and tolerates mismatches and insertions and deletions.

(Short (unspliced) aligners) (Alignment tools)
WHAM WHAM is a high-throughput sequence alignment tool developed at University of Wisconsin-Madison. It aligns short DNA sequences (reads) to the whole human genome at a rate of over 1500 million 60bit/s reads per hour, which is one to two orders of magnitudes faster than the leading state-of-the-art techniques.

(Short (unspliced) aligners) (Alignment tools)
Erange is a tool to alignment and data quantification to mammalian transcriptomes.

(Spliced aligners) (Alignment tools)
IsoformEx

(Spliced aligners) (Alignment tools)
MapAL

(Spliced aligners) (Alignment tools)
OSA

(Spliced aligners) (Alignment tools)
RNA-MATE is a computational pipeline for alignment of data from Applied Biosystems SOLID system. Provides the possibility of quality control and trimming of reads. The genome alignments are performed using mapreads and the splice junctions are identified based on a library of known exon-junction sequences. This tool allows visualization of alignments and tag counting.

(Spliced aligners) (Alignment tools)
RUM performs alignment based on a pipeline, being able to manipulate reads with splice junctions, using Bowtie and Blat. The flowchart starts doing alignment against a genome and a transcriptome database executed by Bowtie. The next step is to perform alignment of unmapped sequences to the genome of reference using BLAT. In the final step all alignments are merged to get the final alignment. The input files can be in FASTA or FASTQ format. The output is presented in RUM and SAM format.

(Spliced aligners) (Alignment tools)
RNASEQR.

(Spliced aligners) (Alignment tools)
SAMMate

(Spliced aligners) (Alignment tools)
SpliceSeq

(Spliced aligners) (Alignment tools)
X-Mate

(Spliced aligners) (Alignment tools)
ABMapper

(Spliced aligners) (Alignment tools)
BBMap Uses short kmers to align reads directly to the genome (spanning introns to find novel isoforms) or transcriptome. Highly tolerant of substitution errors and indels, and very fast. Supports output of all SAM tags needed by Cufflinks. No limit to genome size or number of splices per read. Supports Illumina, 454, Sanger, Ion Torrent, PacBio, and Oxford Nanopore reads, paired or single-ended. Does not use any splice-site-finding heuristics optimized for a single taxonomic branch, but rather finds optimally-scoring multi-affine-transform global alignments, and thus is ideal for studying new organisms with no annotation and unknown splice motifs. Open-source, written in pure Java; supports all platforms with no recompilation and no other dependencies.

(Spliced aligners) (Alignment tools)
ContextMap was developed to overcome some limitations of other mapping approaches, such as resolution of ambiguities. The central idea of this tool is to consider reads in gene expression context, improving this way alignment accuracy. ContextMap can be used as a stand-alone program and supported by mappers producing a SAM file in the output (e.g.: TopHat or MapSplice). In stand-alone mode aligns reads to a genome, to a transcriptome database or both.

(Spliced aligners) (Alignment tools)
CRAC propose a novel way of analyzing reads that integrates genomic locations and local coverage, and detect candidate mutations, indels, splice or fusion junctions in each single read. Importantly, CRAC improves its predictive performance when supplied with e.g. 200 nt reads and should fit future needs of read analyses.

(Spliced aligners) (Alignment tools)
GSNAP

(Spliced aligners) (Alignment tools)
GMAP A Genomic Mapping and Alignment Program for mRNA and EST Sequences.

(Spliced aligners) (Alignment tools)
HISAT HISAT is a fast and sensitive spliced alignment program for mapping RNA-seq reads. In addition to one global FM index that represents a whole genome, HISAT uses a large set of small FM indexes that collectively cover the whole genome (each index represents a genomic region of ~64,000 bp and ~48,000 indexes are needed to cover the human genome). These small indexes (called local indexes) combined with several alignment strategies enable effective alignment of RNA-seq reads, in particular, reads spanning multiple exons. The memory footprint of HISAT is relatively low (~4.3GB for the human genome). We have developed HISAT based on the Bowtie2 implementation to handle most of the operations on the FM index.

(Spliced aligners) (Alignment tools)
HISAT2 HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Based on an extension of BWT for graphs [Sirén et al. 2014], we designed and implemented a graph FM index (GFM), an original approach and its first implementation to the best of our knowledge. In addition to using one global GFM index that represents a population of human genomes, HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome (each index representing a genomic region of 56 Kbp, with 55,000 indexes needed to cover the human population). These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. This new indexing scheme is called a Hierarchical Graph FM index (HGFM).

(Spliced aligners) (Alignment tools)
HMMSplicer can identify canonical and non-canonical splice junctions in short-reads. Firstly, unspliced reads are removed with Bowtie. After that, the remaining reads are one at a time divided in half, then each part is seeded against a genome and the exon borders are determined based on the Hidden Markov Model. A quality score is assigned to each junction, useful to detect false positive rates.

(Spliced aligners) (Alignment tools)
MapSplice

(Spliced aligners) (Alignment tools)
PALMapper

(Spliced aligners) (Alignment tools)
Pass aligns gapped, ungapped reads and also bisulfite sequencing data. It includes the possibility to filter data before alignment (remotion of adapters). Pass uses Needleman-Wunsch and Smith-Waterman algorithms, and performs alignment in 3 stages: scanning positions of seed sequences in the genome, testing the contiguous regions and finally refining the alignment.

(Spliced aligners) (Alignment tools)
PASSion

(Spliced aligners) (Alignment tools)
PASTA

(Spliced aligners) (Alignment tools)
QPALMA predicts splice junctions supported on machine learning algorithms. In this case the training set is a set of spliced reads with quality information and already known alignments.

(Spliced aligners) (Alignment tools)
RAZER : reads aligner for SNPs and editing sites of RNA.

(Spliced aligners) (Alignment tools)
SeqSaw

(Spliced aligners) (Alignment tools)
SoapSplice A tool for genome-wide ab initio detection of splice junction sites from RNA-Seq, a method using new generation sequencing technologies to sequence the messenger RNA.

(Spliced aligners) (Alignment tools)
SpliceMap

(Spliced aligners) (Alignment tools)
SplitSeek

(Spliced aligners) (Alignment tools)
SuperSplat was developed to find all type of splice junctions. The algorithm splits each read in all possible two-chunk combinations in an iterative way, and alignment is tried to each chunck. Output in "Supersplat" format.

(Spliced aligners) (Alignment tools)
MapNext

(Spliced aligners) (Alignment tools)
OLego

(Spliced aligners) (Alignment tools)
STAR is a tool that employs "sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure", detects canonical, non-canonical splices junctions and chimeric-fusion sequences. It is already adapted to align long reads (third-generation sequencing technologies) and can reach speeds of 45 million paired reads per hour per processor.

(Spliced aligners) (Alignment tools)
Subjunc is a specialized version of Subread. It uses all mappable regions in an RNA-seq read to discover exons and exon-exon junctions. It uses the donor/receptor signals to find the exact splicing locations. Subjunc yields full alignments for every RNA-seq read including exon-spanning reads, in addition to the discovered exon-exon junctions. Subjunc should be used for the purpose of junction detection and genomic variation detection in RNA-seq data.

(Spliced aligners) (Alignment tools)
TopHat is prepared to find de novo junctions. TopHat aligns reads in two steps. Firstly, unspliced reads are aligned with Bowtie. After, the aligned reads are assembled with Maq resulting islands of sequences. Secondly, the splice junctions are determined based on the initially unmapped reads and the possible canonical donor and acceptor sites within the island sequences.

(Spliced aligners) (Alignment tools)
G.Mo.R-Se is a method that uses RNA-Seq reads to build de novo gene models.

(Spliced aligners) (Alignment tools)
AlignerBoost is a generalized software toolkit for boosting Next-Gen sequencing mapping precision using a Bayesian-based mapping quality framework.

(Evaluation of alignment tools) (Alignment tools)
CADBURE Bioinformatics tool for evaluating aligner performance on your RNA-Seq dataset.

(Evaluation of alignment tools) (Alignment tools)
QualiMap : Evaluating next generation sequencing alignment data.

(Evaluation of alignment tools) (Alignment tools)
RNAseqEVAL A collection of tools for evaluating RNA seq mapping.

(Evaluation of alignment tools) (Alignment tools)
Teaser: Individualized benchmarking and optimization of read mapping results for NGS data.

(Evaluation of alignment tools) (Alignment tools)
ABSSeq a new RNA-Seq analysis method based on modelling absolute expression differences.

(General tools) (Normalization, quantitative analysis and differential expression)
ALDEx2 is a tool for comparative analysis of high-throughput sequencing data. ALDEx2 uses compositional data analysis and can be applied to RNAseq, 16S rRNA gene sequencing, metagenomic sequencing, and selective growth experiments.

(General tools) (Normalization, quantitative analysis and differential expression)
Alexa-Seq is a pipeline that makes possible to perform gene expression analysis, transcript specific expression analysis, exon junction expression and quantitative alternative analysis. Allows wide alternative expression visualization, statistics and graphs.

(General tools) (Normalization, quantitative analysis and differential expression)
ARH-seq – identification of differential splicing in RNA-seq data.

(General tools) (Normalization, quantitative analysis and differential expression)
ASC

(General tools) (Normalization, quantitative analysis and differential expression)
Ballgown

(General tools) (Normalization, quantitative analysis and differential expression)
BaySeq is a Bioconductor package to identify differential expression using next-generation sequencing data, via empirical Bayesian methods. There is an option of using the "snow" package for parallelisation of computer data processing, recommended when dealing with large data sets.

(General tools) (Normalization, quantitative analysis and differential expression)
GMNB is a Bayesian method to temporal gene differential expression analysis across different phenotypes or treatment conditions that naturally handles the heterogeneity of sequencing depth in different samples, removing the need for ad-hoc normalization.

(General tools) (Normalization, quantitative analysis and differential expression)
BBSeq

(General tools) (Normalization, quantitative analysis and differential expression)
BitSeq (Bayesian Inference of Transcripts from Sequencing Data) is an application for inferring expression levels of individual transcripts from sequencing (RNA-Seq) data and estimating differential expression (DE) between conditions.

(General tools) (Normalization, quantitative analysis and differential expression)
CEDER Accurate detection of differentially expressed genes by combining significance of exons using RNA-Seq.

(General tools) (Normalization, quantitative analysis and differential expression)
CPTRA The CPTRA package is for analyzing transcriptome sequencing data from different sequencing platforms. It combines advantages of 454, Illumina GAII, or other platforms and can perform sequence tag alignment and annotation, expression quantification tasks.

(General tools) (Normalization, quantitative analysis and differential expression)
casper is a Bioconductor package to quantify expression at the isoform level. It combines using informative data summaries, flexible estimation of experimental biases and statistical precision considerations which (reportedly) provide substantial reductions in estimation error.

(General tools) (Normalization, quantitative analysis and differential expression)
Cufflinks/Cuffdiff is appropriate to measure global de novo transcript isoform expression. It performs assembly of transcripts, estimation of abundances and determines differential expression (Cuffdiff) and regulation in RNA-Seq samples.

(General tools) (Normalization, quantitative analysis and differential expression)
DESeq is a Bioconductor package to perform differential gene expression analysis based on negative binomial distribution.

(General tools) (Normalization, quantitative analysis and differential expression)
DEGSeq

(General tools) (Normalization, quantitative analysis and differential expression)
Derfinder Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach.

(General tools) (Normalization, quantitative analysis and differential expression)
DEvis is a powerful, integrated solution for the analysis of differential expression data. Using DESeq2 as a framework, DEvis provides a wide variety of tools for data manipulation, visualization, and project management.

(General tools) (Normalization, quantitative analysis and differential expression)
DEXSeq is Bioconductor package that finds differential differential exon usage based on RNA-Seq exon counts between samples. DEXSeq employs negative binomial distribution, provides options to visualization and exploration of the results.

(General tools) (Normalization, quantitative analysis and differential expression)
DEXUS is a Bioconductor package that identifies differentially expressed genes in RNA-Seq data under all possible study designs such as studies without replicates, without sample groups, and with unknown conditions. In contrast to other methods, DEXUS does not need replicates to detect differentially expressed transcripts, since the replicates (or conditions) are estimated by the EM method for each transcript.

(General tools) (Normalization, quantitative analysis and differential expression)
DGEclust is a Python package for clustering expression data from RNA-seq, CAGE and other NGS assays using a Hierarchical Dirichlet Process Mixture Model. The estimated cluster configurations can be post-processed in order to identify differentially expressed genes and for generating gene- and sample-wise dendrograms and heatmaps.

(General tools) (Normalization, quantitative analysis and differential expression)
DiffSplice is a method for differential expression detection and visualization, not dependent on gene annotations. This method is supported on identification of alternative splicing modules (ASMs) that diverge in the different isoforms. A non-parametric test is applied to each ASM to identify significant differential transcription with a measured false discovery rate.

(General tools) (Normalization, quantitative analysis and differential expression)
EBSeq is a Bioconductor package for identifying genes and isoforms differentially expressed (DE) across two or more biological conditions in an RNA-seq experiment. It also can be used to identify DE contigs after performing de novo transcriptome assembly. While performing DE analysis on isoforms or contigs, different isoform/contig groups have varying estimation uncertainties. EBSeq models the varying uncertainties using an empirical Bayes model with different priors.

(General tools) (Normalization, quantitative analysis and differential expression)
EdgeR is a R package for analysis of differential expression of data from DNA sequencing methods, like RNA-Seq, SAGE or ChIP-Seq data. edgeR employs statistical methods supported on negative binomial distribution as a model for count variability.

(General tools) (Normalization, quantitative analysis and differential expression)
EdgeRun an R package for sensitive, functionally relevant differential expression discovery using an unconditional exact test.

(General tools) (Normalization, quantitative analysis and differential expression)
EQP The exon quantification pipeline (EQP): a comprehensive approach to the quantification of gene, exon and junction expression from RNA-seq data.

(General tools) (Normalization, quantitative analysis and differential expression)
ESAT The End Sequence Analysis Toolkit (ESAT) is specially designed to be applied for quantification of annotation of specialized RNA-Seq gene libraries that target the 5' or 3' ends of transcripts.

(General tools) (Normalization, quantitative analysis and differential expression)
eXpress performance includes transcript-level RNA-Seq quantification, allele-specific and haplotype analysis and can estimate transcript abundances of the multiple isoforms present in a gene. Although could be coupled directly with aligners (like Bowtie), eXpress can also be used with de novo assemblers and thus is not needed a reference genome to perform alignment. It runs on Linux, Mac and Windows.

(General tools) (Normalization, quantitative analysis and differential expression)
ERANGE performs alignment, normalization and quantification of expressed genes.

(General tools) (Normalization, quantitative analysis and differential expression)
featureCounts an efficient general-purpose read quantifier.

(General tools) (Normalization, quantitative analysis and differential expression)
FDM

(General tools) (Normalization, quantitative analysis and differential expression)
FineSplice Enhanced splice junction detection and estimation from RNA-Seq data.

(General tools) (Normalization, quantitative analysis and differential expression)
GFOLD Generalized fold change for ranking differentially expressed genes from RNA-seq data.

(General tools) (Normalization, quantitative analysis and differential expression)
globalSeq Global test for counts: testing for association between RNA-Seq and high-dimensional data.

(General tools) (Normalization, quantitative analysis and differential expression)
GPSeq This is a software tool to analyze RNA-seq data to estimate gene and exon expression, identify differentially expressed genes, and differentially spliced exons.

(General tools) (Normalization, quantitative analysis and differential expression)
IsoDOT – Differential RNA-isoform Expression.

(General tools) (Normalization, quantitative analysis and differential expression)
Limma Limma powers differential expression analyses for RNA-sequencing and microarray studies.

(General tools) (Normalization, quantitative analysis and differential expression)
LPEseq accurately test differential expression with a limited number of replicates.

(General tools) (Normalization, quantitative analysis and differential expression)
Kallisto "Kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. On benchmarks with standard RNA-Seq data, kallisto can quantify 30 million human reads in less than 3 minutes on a Mac desktop computer using only the read sequences and a transcriptome index that itself takes less than 10 minutes to build."

(General tools) (Normalization, quantitative analysis and differential expression)
MATS Multivariate Analysis of Transcript Splicing (MATS).

(General tools) (Normalization, quantitative analysis and differential expression)
MAPTest provides a general testing framework for differential expression analysis of RNA-Seq time course experiment. Method of the pack is based on latent negative-binomial Gaussian mixture model. The proposed test is optimal in the maximum average power. The test allows not only identification of traditional DE genes but also testing of a variety of composite hypotheses of biological interest.

(General tools) (Normalization, quantitative analysis and differential expression)
MetaDiff Differential isoform expression analysis using random-effects meta-regression.

(General tools) (Normalization, quantitative analysis and differential expression)
metaseqR is a Bioconductor package that detects differentially expressed genes from RNA-Seq data by combining six statistical algorithms using weights estimated from their performance with simulated data estimated from real data, either public or user-based. In this way, metaseqR optimizes the tradeoff between precision and sensitivity. In addition, metaseqR creates a detailed and interactive report with a variety of diagnostic and exploration plots and auto-generated text.

(General tools) (Normalization, quantitative analysis and differential expression)
MMSEQ is a pipeline for estimating isoform expression and allelic imbalance in diploid organisms based on RNA-Seq. The pipeline employs tools like Bowtie, TopHat, ArrayExpressHTS and SAMtools. Also, edgeR or DESeq to perform differential expression.

(General tools) (Normalization, quantitative analysis and differential expression)
MultiDE

(General tools) (Normalization, quantitative analysis and differential expression)
Myrna is a pipeline tool that runs in a cloud environment (Elastic MapReduce) or in a unique computer for estimating differential gene expression in RNA-Seq datasets. Bowtie is employed for short read alignment and R algorithms for interval calculations, normalization, and statistical processing.

(General tools) (Normalization, quantitative analysis and differential expression)
NEUMA is a tool to estimate RNA abundances using length normalization, based on uniquely aligned reads and mRNA isoform models. NEUMA uses known transcriptome data available in databases like RefSeq.

(General tools) (Normalization, quantitative analysis and differential expression)
NOISeq NOISeq is a non-parametric approach for the identification of differentially expressed genes from count data or previously normalized count data. NOISeq empirically models the noise distribution of count changes by contrasting fold-change differences (M) and absolute expression differences (D) for all the features in samples within the same condition.

(General tools) (Normalization, quantitative analysis and differential expression)
NPEBseq is a nonparametric empirical Bayesian-based method for differential expression analysis.

(General tools) (Normalization, quantitative analysis and differential expression)
NSMAP allows inference of isoforms as well estimation of expression levels, without annotated information. The exons are aligned and splice junctions are identified using TopHat. All the possible isoforms are computed by a combination of the detected exons.

(General tools) (Normalization, quantitative analysis and differential expression)
NURD an implementation of a new method to estimate isoform expression from non-uniform RNA-seq data.

(General tools) (Normalization, quantitative analysis and differential expression)
PANDORA An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms.

(General tools) (Normalization, quantitative analysis and differential expression)
PennSeq PennSeq: accurate isoform-specific gene expression quantification in RNA-Seq by modeling non-uniform read distribution.

(General tools) (Normalization, quantitative analysis and differential expression)
Quark Quark enables semi-reference-based compression of RNA-seq data.

(General tools) (Normalization, quantitative analysis and differential expression)
QuasR Quantify and Annotate Short Reads in R.

(General tools) (Normalization, quantitative analysis and differential expression)
RapMap A Rapid, Sensitive and Accurate Tool for Mapping RNA-seq Reads to Transcriptomes.

(General tools) (Normalization, quantitative analysis and differential expression)
RNAeXpress Can be run with Java GUI or command line on Mac, Windows, and Linux. It can be configured to perform read counting, feature detection or GTF comparison on mapped rnaseq data.

(General tools) (Normalization, quantitative analysis and differential expression)
Rcount Rcount: simple and flexible RNA-Seq read counting.

(General tools) (Normalization, quantitative analysis and differential expression)
rDiff is a tool that can detect differential RNA processing (e.g. alternative splicing, polyadenylation or ribosome occupancy).

(General tools) (Normalization, quantitative analysis and differential expression)
RNASeqPower Calculating samples Size estimates for RNA Seq studies. R package version.

(General tools) (Normalization, quantitative analysis and differential expression)
RNA-Skim RNA-Skim: a rapid method for RNA-Seq quantification at transcript-level.

(General tools) (Normalization, quantitative analysis and differential expression)
rSeq rSeq is a set of tools for RNA-Seq data analysis. It consists of programs that deal with many aspects of RNA-Seq data analysis, such as read quality assessment, reference sequence generation, sequence mapping, gene and isoform expressions (RPKMs) estimation, etc.

(General tools) (Normalization, quantitative analysis and differential expression)
RSEM

(General tools) (Normalization, quantitative analysis and differential expression)
rQuant is a web service (Galaxy (computational biology) installation) that determines abundances of transcripts per gene locus, based on quadratic programming. rQuant is able to evaluate biases introduced by experimental conditions. A combination of tools is employed: PALMapper (reads alignment), mTiM and mGene (inference of new transcripts).

(General tools) (Normalization, quantitative analysis and differential expression)
Salmon is a software tool for computing transcript abundance from RNA-seq data using either an alignment-free (based directly on the raw reads) or an alignment-based (based on pre-computed alignments) approach. It uses an online stochastic optimization approach to maximize the likelihood of the transcript abundances under the observed data. The software itself is capable of making use of many threads to produce accurate quantification estimates quickly. It is part of the Sailfish suite of software, and is the successor to the Sailfish tool.

(General tools) (Normalization, quantitative analysis and differential expression)
SAJR is a java-written read counter and R-package for differential splicing analysis. It uses junction reads to estimate exon exclusion and reads mapped within exon to estimate its inclusion. SAJR models it by GLM with quasibinomial distribution and uses log likelihood test to assess significance.

(General tools) (Normalization, quantitative analysis and differential expression)
Scotty Performs power analysis to estimate the number of replicates and depth of sequencing required to call differential expression.

(General tools) (Normalization, quantitative analysis and differential expression)
Seal alignment-free algorithm to quantify sequence expression by matching kmers between raw reads and a reference transcriptome. Handles paired reads and alternate isoforms, and uses little memory. Accepts all common read formats, and outputs read counts, coverage, and FPKM values per reference sequence. Open-source, written in pure Java; supports all platforms with no recompilation and no other dependencies. Distributed with BBMap. (Seal - Sequence Expression AnaLyzer - is unrelated to the SEAL distributed short-read aligner.)

(General tools) (Normalization, quantitative analysis and differential expression)
semisup Semi-supervised mixture model: detecting SNPs with interactive effects on a quantitative trait

(General tools) (Normalization, quantitative analysis and differential expression)
Sleuth is a program for analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto.

(General tools) (Normalization, quantitative analysis and differential expression)
SplicingCompass differential splicing detection using RNA-Seq data.

(General tools) (Normalization, quantitative analysis and differential expression)
sSeq The purpose of this R package is to discover the genes that are differentially expressed between two conditions in RNA-seq experiments.

(General tools) (Normalization, quantitative analysis and differential expression)
StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. It was designed as a successor to Cufflinks (its developers include some of the Cufflinks developers) and has many of the same features, but runs far faster and in far less memory.

(General tools) (Normalization, quantitative analysis and differential expression)
TIGAR Transcript isoform abundance estimation method with gapped alignment of RNA-Seq data by variational Bayesian inference.

(General tools) (Normalization, quantitative analysis and differential expression)
TimeSeq Detecting Differentially Expressed Genes in Time Course RNA-Seq Data.

(General tools) (Normalization, quantitative analysis and differential expression)
WemIQ is a software tool to quantify isoform expression and exon splicing ratios from RNA-seq data accurately and robustly.

(General tools) (Normalization, quantitative analysis and differential expression)
CompcodeR RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods.

(Evaluation of quantification and differential expression) (Normalization, quantitative analysis and differential expression)
DEAR-O Differential Expression Analysis based on RNA-seq data – Online.

(Evaluation of quantification and differential expression) (Normalization, quantitative analysis and differential expression)
PROPER comprehensive power evaluation for differential expression using RNA-seq.

(Evaluation of quantification and differential expression) (Normalization, quantitative analysis and differential expression)
RNAontheBENCH computational and empirical resources for benchmarking RNAseq quantification and differential expression methods.

(Evaluation of quantification and differential expression) (Normalization, quantitative analysis and differential expression)
rnaseqcomp Several quantitative and visualized benchmarks for RNA-seq quantification pipelines. Two-condition quantifications for genes, transcripts, junctions or exons by each pipeline with nessasery meta information should be organizd into numeric matrices in order to proceed the evaluation.

(Evaluation of quantification and differential expression) (Normalization, quantitative analysis and differential expression)
DEB is a web-interface/pipeline that permits to compare results of significantly expressed genes from different tools. Currently are available three algorithms: edgeR, DESeq and bayseq.

(Multi-tool solutions) (Normalization, quantitative analysis and differential expression)
SARTools A DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data.

(Multi-tool solutions) (Normalization, quantitative analysis and differential expression)
TeXP is a Transposable Element quantification pipeline that deconvolves pervasive transcription from autonomous transcription of LINE-1 elements.

(Transposable Element expression) (Normalization, quantitative analysis and differential expression)
ActiveSite by Cofactor Genomics

(Commercial solutions) (Workbench (analysis pipeline / integrated solutions))
Avadis NGS (currently Strand NGS)

(Commercial solutions) (Workbench (analysis pipeline / integrated solutions))
BaseSpace by Illumina

(Commercial solutions) (Workbench (analysis pipeline / integrated solutions))
Biowardrobe an integrated platform for analysis of epigenomics and transcriptomics data.

(Commercial solutions) (Workbench (analysis pipeline / integrated solutions))
CLC Genomics Workbench

(Commercial solutions) (Workbench (analysis pipeline / integrated solutions))
DNASTAR

(Commercial solutions) (Workbench (analysis pipeline / integrated solutions))
ERGO

(Commercial solutions) (Workbench (analysis pipeline / integrated solutions))
Genedata

(Commercial solutions) (Workbench (analysis pipeline / integrated solutions))
GeneSpring GX

(Commercial solutions) (Workbench (analysis pipeline / integrated solutions))
Genevestigator by Nebion (basic version is for free for academic researchers).

(Commercial solutions) (Workbench (analysis pipeline / integrated solutions))
geospiza

(Commercial solutions) (Workbench (analysis pipeline / integrated solutions))
Golden Helix

(Commercial solutions) (Workbench (analysis pipeline / integrated solutions))
Maverix Biomics

(Commercial solutions) (Workbench (analysis pipeline / integrated solutions))
NextGENe

(Commercial solutions) (Workbench (analysis pipeline / integrated solutions))
OmicsOffice

(Commercial solutions) (Workbench (analysis pipeline / integrated solutions))
Partek Flow Comprehensive single cell analysis within an intuitive interface.

(Commercial solutions) (Workbench (analysis pipeline / integrated solutions))
Qlucore. Easy to use for analysis and visualization. One button import of BAM files.

(Commercial solutions) (Workbench (analysis pipeline / integrated solutions))
ArrayExpressHTS is a BioConductor package that allows preprocessing, quality assessment and estimation of expression of RNA-Seq datasets. It can be run remotely at the European Bioinformatics Institute cloud or locally. The package makes use of several tools: ShortRead (quality control), Bowtie, TopHat or BWA (alignment to a reference genome), SAMtools format, Cufflinks or MMSEQ (expression estimation).

(Open (free) source solutions) (Workbench (analysis pipeline / integrated solutions))
BioJupies is a web-based platform that provides complete RNA-seq analysis solution from free alignment service to a complete data analysis report delivered as an interactive Jupyter Notebook.

(Open (free) source solutions) (Workbench (analysis pipeline / integrated solutions))
BioQueue is a web-based queue engine designed preferentially to improve the efficiency and robustness of job execution in bioinformatics research by estimating the system resources required by a certain job. At the same time, BioQueue also aims to promote the accessibility and reproducibility of data analysis in biomedical research. Implemented by Python 2.7, BioQueue can work in both POSIX compatible systems (Linux, Solaris, OS X, etc.) and Windows. See also.

(Open (free) source solutions) (Workbench (analysis pipeline / integrated solutions))
BioWardrobe is an integrated package that for analysis of ChIP-Seq and RNA-Seq datasets using a web-based user-friendly GUI. For RNA-Seq Biowardrobe performs mapping, quality control, RPKM estimation and differential expression analysis between samples (groups of samples). Results of differential expression analysis can be integrated with ChIP-Seq data to build average tag density profiles and heat maps. The package makes use of several tools open source tools including STAR and DESeq. See also.

(Open (free) source solutions) (Workbench (analysis pipeline / integrated solutions))
Chipster is a user-friendly analysis software for high-throughput data. It contains over 350 analysis tools for next generation sequencing (NGS), microarray, proteomics and sequence data. Users can save and share automatic analysis workflows, and visualize data interactively using a built-in genome browser and many other visualizations.

(Open (free) source solutions) (Workbench (analysis pipeline / integrated solutions))
DEWE (Differential Expression Workflow Executor) is an open source desktop application that provides a user-friendly GUI for easily executing Differential Expression analyses in RNA-Seq data. Currently, DEWE provides two differential expression analysis workflows: HISAT2, StringTie and Ballgown and Bowtie2, StringTie and R libraries (Ballgown and edgeR). It runs in Linux, Windows and Mac OS X.

(Open (free) source solutions) (Workbench (analysis pipeline / integrated solutions))
easyRNASeq Calculates the coverage of high-throughput short-reads against a genome of reference and summarizes it per feature of interest (e.g. exon, gene, transcript). The data can be normalized as 'RPKM' or by the 'DESeq' or 'edgeR' package.

(Open (free) source solutions) (Workbench (analysis pipeline / integrated solutions))
ExpressionPlot

(Open (free) source solutions) (Workbench (analysis pipeline / integrated solutions))
FASTGenomics is an online platform to share single-cell RNA sequencing data and analyses using reproducible workflows. Gene expression data can be shared meeting European data protection standards (GDPR). FASTGenomics enables the user to upload their own data and generate customized and reproducible workflows for the exploration and analysis of gene expression data (Scholz et al. 2018).

(Open (free) source solutions) (Workbench (analysis pipeline / integrated solutions))
FX FX is a user-Frendly RNA-Seq gene eXpression analysis tool, empowered by the concept of cloud-computing. With FX, you can simply upload your RNA-Seq raw FASTQ data on the cloud, and let the computing infra to do the heavy analysis.

(Open (free) source solutions) (Workbench (analysis pipeline / integrated solutions))
Galaxy: Galaxy is a general purpose workbench platform for computational biology.

(Open (free) source solutions) (Workbench (analysis pipeline / integrated solutions))
GENE-Counter is a Perl pipeline for RNA-Seq differential gene expression analyses. Gene-counter performs alignments with CASHX, Bowtie, BWA or other SAM output aligner. Differential gene expression is run with three optional packages (NBPSeq, edgeR and DESeq) using negative binomial distribution methods. Results are stored in a MySQL database to make possible additional analyses.

(Open (free) source solutions) (Workbench (analysis pipeline / integrated solutions))
GenePattern offers integrated solutions to RNA-Seq analysis (Broad Institute).

(Open (free) source solutions) (Workbench (analysis pipeline / integrated solutions))
GeneProf Freely accessible, easy to use analysis pipelines for RNA-seq and ChIP-seq experiments.

(Open (free) source solutions) (Workbench (analysis pipeline / integrated solutions))
GREIN is an interactive web platform for re-processing and re-analyzing GEO RNA-seq data. GREIN is powered by the back-end computational pipeline for uniform processing of RNA-seq data and the large number (>5,800) of already processed data sets. The front-end user friendly interfaces provide a wealth of user-analytics options including sub-setting and downloading processed data, interactive visualization, statistical power analyses, construction of differential gene expression signatures and their comprehensive functional characterization, connectivity analysis with LINCS L1000 data, etc.

(Open (free) source solutions) (Workbench (analysis pipeline / integrated solutions))
GT-FAR is an RNA seq pipeline that performs RNA-seq QC, alignment, reference free quantification, and splice variant calling. It filters, trims, and sequentially aligns reads to gene models and predicts and validates new splice junctions after which it quantifies expression for each gene, exon, and known/novel splice junction, and Variant Calling.

(Open (free) source solutions) (Workbench (analysis pipeline / integrated solutions))
MultiExperiment Viewer (MeV) is suitable to perform analysis, data mining and visualization of large-scale genomic data. The MeV modules include a variety of algorithms to execute tasks like Clustering and Classification, Student's t-test, Gene Set Enrichment Analysis or Significance Analysis. MeV runs on Java.

(Open (free) source solutions) (Workbench (analysis pipeline / integrated solutions))
NGSUtils is a suite of software tools for working with next-generation sequencing datasets.

(Open (free) source solutions) (Workbench (analysis pipeline / integrated solutions))
Rail-RNA Scalable analysis of RNA-seq splicing and coverage.

(Open (free) source solutions) (Workbench (analysis pipeline / integrated solutions))
RAP RNA-Seq Analysis Pipeline, a new cloud-based NGS web application.

(Open (free) source solutions) (Workbench (analysis pipeline / integrated solutions))
RSEQtools "RSEQtools consists of a set of modules that perform common tasks such as calculating gene expression values, generating signal tracks of mapped reads, and segmenting that signal into actively transcribed regions. In addition to the anonymization afforded by this format it also facilitates the decoupling of the alignment of reads from downstream analyses."

(Open (free) source solutions) (Workbench (analysis pipeline / integrated solutions))
RobiNA provides a user graphical interface to deal with R/BioConductor packages. RobiNA provides a package that automatically installs all required external tools (R/Bioconductor frameworks and Bowtie). This tool offers a diversity of quality control methods and the possibility to produce many tables and plots supplying detailed results for differential expression. Furthermore, the results can be visualized and manipulated with MapMan and PageMan. RobiNA runs on Java version 6.

(Open (free) source solutions) (Workbench (analysis pipeline / integrated solutions))
RseqFlow is an RNA-Seq analysis pipeline which offers an express implementation of analysis steps for RNA sequencing datasets. It can perform pre and post mapping quality control (QC) for sequencing data, calculate expression levels for uniquely mapped reads, identify differentially expressed genes, and convert file formats for ease of visualization.

(Open (free) source solutions) (Workbench (analysis pipeline / integrated solutions))
S-MART handles mapped RNA-Seq data, and performs essentially data manipulation (selection/exclusion of reads, clustering and differential expression analysis) and visualization (read information, distribution, comparison with epigenomic ChIP-Seq data). It can be run on any laptop by a person without computer background. A friendly graphical user interface makes easy the operation of the tools.

(Open (free) source solutions) (Workbench (analysis pipeline / integrated solutions))
Taverna is an open source and domain-independent Workflow Management System – a suite of tools used to design and execute scientific workflows and aid in silico experimentation.

(Open (free) source solutions) (Workbench (analysis pipeline / integrated solutions))
TCW is a Transcriptome Computational Workbench.

(Open (free) source solutions) (Workbench (analysis pipeline / integrated solutions))
TRAPLINE a standardized and automated pipeline for RNA sequencing data analysis, evaluation and annotation.

(Open (free) source solutions) (Workbench (analysis pipeline / integrated solutions))
ViennaNGS A toolbox for building efficient next- generation sequencing analysis pipelines.

(Open (free) source solutions) (Workbench (analysis pipeline / integrated solutions))
wapRNA This is a free web-based application for the processing of high-throughput RNA-Seq data (wapRNA) from next generation sequencing (NGS) platforms, such as Genome Analyzer of Illumina Inc. (Solexa) and SOLiD of Applied Biosystems (SOLiD). wapRNA provides an integrated tool for RNA sequence, refers to the use of High-throughput sequencing technologies to sequence cDNAs in order to get information about a sample's RNA content.

(Open (free) source solutions) (Workbench (analysis pipeline / integrated solutions))
Alternative Splicing Analysis Tool Package(ASATP) Alternative splicing analysis tool package (ASATP) includes a series of toolkits to analyze alternative splicing events, which could be used to detect and visualized alternative splicing events, check ORF changes, assess regulations of alternative splicing and do statistical analysis.

(General tools) (Alternative splicing analysis)
Asprofile is a suite of programs for extracting, quantifying and comparing alternative splicing (AS) events from RNA-seq data.

(General tools) (Alternative splicing analysis)
AStalavista The AStalavista web server extracts and displays alternative splicing (AS) events from a given genomic annotation of exon-intron gene coordinates. By comparing all given transcripts, AStalavista detects the variations in their splicing structure and identify all AS events (like exon skipping, alternate donor, etc.) by assigning to each of them an AS code.

(General tools) (Alternative splicing analysis)
CLASS2 accurate and efficient splice variant annotation from RNA-seq reads.

(General tools) (Alternative splicing analysis)
Cufflinks/Cuffdiff

(General tools) (Alternative splicing analysis)
DEXseq Inference of differential exon usage in RNA-Seq.

(General tools) (Alternative splicing analysis)
Diceseq Statistical modeling of isoform splicing dynamics from RNA-seq time series data.

(General tools) (Alternative splicing analysis)
EBChangepoint An empirical Bayes change-point model for identifying 3′ and 5′ alternative splicing by RNA-Seq.

(General tools) (Alternative splicing analysis)
Eoulsan A versatile framework dedicated to high throughput sequencing data analysis. Allows automated analysis (mapping, counting and differencial analysis with DESeq2).

(General tools) (Alternative splicing analysis)
GESS for de novo detection of exon-skipping event sites from raw RNA-seq reads.

(General tools) (Alternative splicing analysis)
LeafCutter a suite of novel methods that allow identification and quantication of novel and existing alternative splicing events by focusing on intron excisions.

(General tools) (Alternative splicing analysis)
LEMONS A Tool for the Identification of Splice Junctions in Transcriptomes of Organisms Lacking Reference Genomes.

(General tools) (Alternative splicing analysis)
MAJIQ. Modeling Alternative Junction Inclusion Quantification.

(General tools) (Alternative splicing analysis)
MATS Multivariate Analysis of Transcript Splicing (MATS).

(General tools) (Alternative splicing analysis)
MISO quantifies the expression level of splice variants from RNA-Seq data and is able to recognize differentially regulated exons/isoforms across different samples. MISO uses a probabilistic method (Bayesian inference) to calculate the probability of the reads origin.

(General tools) (Alternative splicing analysis)
Rail-RNA Scalable analysis of RNA-seq splicing and coverage.

(General tools) (Alternative splicing analysis)
RPASuite RPASuite (RNA Processing Analysis Suite) is a computational pipeline to identify differentially and coherently processed transcripts using RNA-seq data obtained from multiple tissue or cell lines.

(General tools) (Alternative splicing analysis)
RSVP RSVP is a software package for prediction of alternative isoforms of protein-coding genes, based on both genomic DNA evidence and aligned RNA-seq reads. The method is based on the use of ORF graphs, which are more general than the splice graphs used in traditional transcript assembly.

(General tools) (Alternative splicing analysis)
SAJR calculates the number of the reads that confirms segment (part of gene between two nearest splice sites) inclusion or exclusion and then model these counts by GLM with quasibinomial distribution to account for biological variability.

(General tools) (Alternative splicing analysis)
SGSeq A R package to de novo prediction of splicing events.

(General tools) (Alternative splicing analysis)
SplAdder Identification, quantification and testing of alternative splicing events from RNA-Seq data.

(General tools) (Alternative splicing analysis)
SpliceGrapher Prediction of novel alternative splicing events from RNA-Seq data. Also includes graphical tools for visualizing splice graphs.

(General tools) (Alternative splicing analysis)
SpliceJumper a classification-based approach for calling splicing junctions from RNA-seq data.

(General tools) (Alternative splicing analysis)
SplicePie is a pipeline to analyze non-sequential and multi-step splicing. SplicePie contains three major analysis steps: analyzing the order of splicing per sample, looking for recursive splicing events per sample and summarizing predicted recursive splicing events for all analyzed sample (it is recommended to use more samples for higher reliability). The first two steps are performed individually on each sample and the last step looks at the overlap in all samples. However, the analysis can be run on one sample as well.

(General tools) (Alternative splicing analysis)
SplicePlot is a tool for visualizing alternative splicing and the effects of splicing quantitative trait loci (sQTLs) from RNA-seq data. It provides a simple command line interface for drawing sashimi plots, hive plots, and structure plots of alternative splicing events from .bam, .gtf, and .vcf files.

(General tools) (Alternative splicing analysis)
SpliceR An R package for classification of alternative splicing and prediction of coding potential from RNA-seq data.

(General tools) (Alternative splicing analysis)
SpliceSEQ SpliceViewer is a Java application that allows researchers to investigate alternative mRNA splicing patterns in data from high-throughput mRNA sequencing studies. Sequence reads are mapped to splice graphs that unambiguously quantify the inclusion level of each exon and splice junction. The graphs are then traversed to predict the protein isoforms that are likely to result from the observed exon and splice junction reads. UniProt annotations are mapped to each protein isoform to identify potential functional impacts of alternative splicing.

(General tools) (Alternative splicing analysis)
SpliceTrap is a statistical tool for the quantification of exon inclusion ratios from RNA-seq data.

(General tools) (Alternative splicing analysis)
Splicing Express – a software suite for alternative splicing analysis using next-generation sequencing data.

(General tools) (Alternative splicing analysis)
SUPPA This tool generates different Alternative Splicing (AS) events and calculates the PSI ("Percentage Spliced In") value for each event exploiting the fast quantification of transcript abundances from multiple samples.

(General tools) (Alternative splicing analysis)
SwitchSeq identifies extreme changes in splicing (switch events).

(General tools) (Alternative splicing analysis)
Portcullis identification of genuine splice junctions.

(General tools) (Alternative splicing analysis)
TrueSight A Self-training Algorithm for Splice Junction Detection using RNA-seq.

(General tools) (Alternative splicing analysis)
Vast-tools A toolset for profiling alternative splicing events in RNA-Seq data.

(General tools) (Alternative splicing analysis)
IRcall / IRclassifier IRcall is a computational tool for IR event detection from RNA-Seq data. IRclassifier is a supervised machine learning-based approach for IR event detection from RNA-Seq data.

(Intron retention analysis) (Alternative splicing analysis)
IsoformSwitchAnalyzeR IsoformSwitchAnalyzeR is an R package that enables statistical identification of isoform switches with predicted functional consequences where the consequences of interest can be chosen from a long list but includes gain/loss of protein domains, signal peptides changes in NMD sensitivity. IsoformSwitchAnalyzeR is made for post analysis of data from any full length isoform/transcript quantification tool but directly support Cufflinks/Cuffdiff, RSEM Kallisto and Salmon.

(Differential isoform/transcript usage) (Alternative splicing analysis)
DRIMSeq An R package that utilizes generalized linear modeling (GLM) to identify isoform switches from estimated isoform count data.

(Differential isoform/transcript usage) (Alternative splicing analysis)
BayesDRIMSeq An R package containing a Bayesian implementation of DRIMSeq.

(Differential isoform/transcript usage) (Alternative splicing analysis)
Cufflinks/Cuffdiff Full length isoform/transcript quantification and differential analysis tool which amongst other test for changes in usage for isoform belonging to the same primary transcript (sharing a TSS) via a one-sided t-test based on the asymptotic of the Jensen-Shannon metric.

(Differential isoform/transcript usage) (Alternative splicing analysis)
rSeqNP An R package that implements a non-parametric approach to test for differential expression and splicing from RNA-Seq data.

(Differential isoform/transcript usage) (Alternative splicing analysis)
Isolator Full length isoform/transcript quantification and differential analysis tool which analyses all samples in an experiment in unison using a simple Bayesian hierarchical model. Can identify differential isoform usage by testing for probability of monotonic splicing.

(Differential isoform/transcript usage) (Alternative splicing analysis)
Arriba is an ultrafast fusion detection algorithm based on the STAR RNA-Seq aligner. It is the winner of the DREAM Challenge about fusion detection. Arriba can also detect exon duplications, Circular RNAs, and breakpoints in introns and intergenic regions. (Fusion genes/chimeras/translocation finders/structural variations)
Bellerophontes (Fusion genes/chimeras/translocation finders/structural variations)
BreakDancer (Fusion genes/chimeras/translocation finders/structural variations)
BreakFusion (Fusion genes/chimeras/translocation finders/structural variations)
ChimeraScan (Fusion genes/chimeras/translocation finders/structural variations)
EBARDenovo (Fusion genes/chimeras/translocation finders/structural variations)
EricScript (Fusion genes/chimeras/translocation finders/structural variations)
DEEPEST is a statistical fusion detection algorithm. DEEPEST can also detect Circular RNAs. (Fusion genes/chimeras/translocation finders/structural variations)
DeFuse DeFuse is a software package for gene fusion discovery using RNA-Seq data. (Fusion genes/chimeras/translocation finders/structural variations)
FusionAnalyser FusionAnalyser uses paired reads mapping to different genes (Bridge reads). (Fusion genes/chimeras/translocation finders/structural variations)
FusionCatcher FusionCatcher searches for novel/known somatic fusion genes, translocations, and chimeras in RNA-seq data (stranded/unstranded paired-end reads from Illumina NGS platforms) from diseased samples. (Fusion genes/chimeras/translocation finders/structural variations)
FusionHunter identifies fusion transcripts without depending on already known annotations. It uses Bowtie as a first aligner and paired-end reads. (Fusion genes/chimeras/translocation finders/structural variations)
FusionMap FusionMap is a fusion aligner which aligns reads spanning fusion junctions directly to the genome without prior knowledge of potential fusion regions. It detects and characterizes fusion junctions at base-pair resolution. FusionMap can be applied to detect fusion junctions in both single- and paired-end dataset from either gDNA-Seq or RNA-Seq studies. (Fusion genes/chimeras/translocation finders/structural variations)
FusionSeq (Fusion genes/chimeras/translocation finders/structural variations)
JAFFA is based on the idea of comparing a transcriptome against a reference transcriptome rather than a genome-centric approach like other fusion finders. (Fusion genes/chimeras/translocation finders/structural variations)
MapSplice (Fusion genes/chimeras/translocation finders/structural variations)
nFuse (Fusion genes/chimeras/translocation finders/structural variations)
Oncomine NGS RNA-Seq Gene Expression Browser. (Fusion genes/chimeras/translocation finders/structural variations)
PRADA (Fusion genes/chimeras/translocation finders/structural variations)
SOAPFuse detects fusion transcripts from human paired-end RNA-Seq data. It outperforms other five similar tools in both computation and fusion detection performance using both real and simulated data. (Fusion genes/chimeras/translocation finders/structural variations)
SOAPfusion (Fusion genes/chimeras/translocation finders/structural variations)
TopHat-Fusion is based on TopHat version and was developed to handle reads resulting from fusion genes. It does not require previous data about known genes and uses Bowtie to align continuous reads. (Fusion genes/chimeras/translocation finders/structural variations)
ViralFusionSeq is high-throughput sequencing (HTS) tool for discovering viral integration events and reconstruct fusion transcripts at single-base resolution. (Fusion genes/chimeras/translocation finders/structural variations)
ViReMa (Viral Recombination Mapper) detects and reports recombination or fusion events in and between virus and host genomes using deep sequencing datasets. (Fusion genes/chimeras/translocation finders/structural variations)
CNVseq detects copy number variations supported on a statistical model derived from array-comparative genomic hybridization. Sequences alignment are performed by BLAT, calculations are executed by R modules and is fully automated using Perl. (Copy number variation identification)
Monocle Differential expression and time-series analysis for single-cell RNA-Seq and qPCR experiments.

(Integrated Packages) (Single cell RNA-Seq)
SCell integrated analysis of single-cell RNA-seq data.

(Integrated Packages) (Single cell RNA-Seq)
Sincell an R/Bioconductor package for statistical assessment of cell-state hierarchies from single-cell RNA-seq.

(Integrated Packages) (Single cell RNA-Seq)
SINCERA A Pipeline for Single-Cell RNA-Seq Profiling Analysis.

(Integrated Packages) (Single cell RNA-Seq)
Celloline A pipeline for mapping and quality assessment single cell RNA-seq data.

(Quality Control and Gene Filtering) (Single cell RNA-Seq)
OEFinder A user interface to identify and visualize ordering effects in single-cell RNA-seq data.

(Quality Control and Gene Filtering) (Single cell RNA-Seq)
SinQC A Method and Tool to Control Single-cell RNA-seq Data Quality.

(Quality Control and Gene Filtering) (Single cell RNA-Seq)
BASICS Understanding changes in gene expression at the single-cell level.

(Normalization) (Single cell RNA-Seq)
GRM Normalization and noise reduction for single cell RNA-seq experiments.

(Normalization) (Single cell RNA-Seq)
ZIFA Dimensionality reduction for zero-inflated single-cell gene expression analysis.

(Dimension Reduction) (Single cell RNA-Seq)
BPSC An R package BPSC for model fitting and differential expression analyses of single-cell RNA-seq.

(Differential Expression) (Single cell RNA-Seq)
MAST a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data.

(Differential Expression) (Single cell RNA-Seq)
SCDE Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis.

(Differential Expression) (Single cell RNA-Seq)
eXpose

(Visualization) (Single cell RNA-Seq)
BEERS Simulator is formatted to mouse or human data, and paired-end reads sequenced on Illumina platform. Beers generates reads starting from a pool of gene models coming from different published annotation origins. Some genes are chosen randomly and afterwards are introduced deliberately errors (like indels, base changes and low quality tails), followed by construction of novel splice junctions. (RNA-Seq simulators)
compcodeR RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods. (RNA-Seq simulators)
CuReSim a customized read simulator. (RNA-Seq simulators)
Flux simulator implements a computer pipeline simulation to mimic a RNA-Seq experiment. All component steps that influence RNA-Seq are taken into account (reverse transcription, fragmentation, adapter ligation, PCR amplification, gel segregation and sequencing) in the simulation. These steps present experimental attributes that can be measured, and the approximate experimental biases are captured. Flux Simulator allows joining each of these steps as modules to analyse different type of protocols. (RNA-Seq simulators)
PBSIM PacBio reads simulator - toward accurate genome assembly. (RNA-Seq simulators)
Polyester This bioconductor package can be used to simulate RNA-seq reads from differential expression experiments with replicates. The reads can then be aligned and used to perform comparisons of methods for differential expression. (RNA-Seq simulators)
RandomReads Generates synthetic reads from a genome with an Illumina or PacBio error model. The reads may be paired or unpaired, with arbitrary length and insert size, output in fasta or fastq, RandomReads has a wide selection of options for mutation rates, with individual settings for substitution, deletion, insertion, and N rates and length distributions, annotating reads with their original, unmutated genomic start and stop location. RandomReads is does not vary expression levels and thus is not designed to simulate RNA-seq experiments, but to test the sensitivity and specificity of RNA-seq aligners with de-novo introns. Includes a tool for grading and generating ROC curves from resultant sam files. Open-source, written in pure Java; supports all platforms with no recompilation and no other dependencies. Distributed with BBMap. (RNA-Seq simulators)
rlsim is a software package for simulating RNA-seq library preparation with parameter estimation. (RNA-Seq simulators)
rnaseqbenchmark A Benchmark for RNA-seq Quantification Pipelines. (RNA-Seq simulators)
rnaseqcomp Benchmarks for RNA-seq Quantification Pipelines. (RNA-Seq simulators)
RSEM Read Simulator RSEM provides users the ‘rsem-simulate-reads’ program to simulate RNA-Seq data based on parameters learned from real data sets. (RNA-Seq simulators)
RNASeqReadSimulator contains a set of simple Python scripts, command line driven. It generates random expression levels of transcripts (single or paired-end), equally simulates reads with a specific positional bias pattern and generates random errors from sequencing platforms. (RNA-Seq simulators)
RNA Seq Simulator RSS takes SAM alignment files from RNA-Seq data and simulates over dispersed, multiple replica, differential, non-stranded RNA-Seq datasets. (RNA-Seq simulators)
SimSeq A Nonparametric Approach to Simulation of RNA-Sequence Datasets. (RNA-Seq simulators)
WGsim Wgsim is a small tool for simulating sequence reads from a reference genome. It is able to simulate diploid genomes with SNPs and insertion/deletion (INDEL) polymorphisms, and simulate reads with uniform substitution sequencing errors. It does not generate INDEL sequencing errors, but this can be partly compensated by simulating INDEL polymorphisms. (RNA-Seq simulators)
Bayesembler Bayesian transcriptome assembly.

(Genome-guided assemblers) (Transcriptome assemblers)
CIDANE a comprehensive isoform discovery and abundance estimation.

(Genome-guided assemblers) (Transcriptome assemblers)
CLASS CLASS is a program for assembling transcripts from RNA-seq reads aligned to a genome. CLASS produces a set of transcripts in three stages. Stage 1 uses linear programming to determine a set of exons for each gene. Stage 2 builds a splice graph representation of a gene, by connecting the exons (vertices) via introns (edges) extracted from spliced read alignments. Stage 3 selects a subset of the candidate transcripts encoded in the graph that can explain all the reads, using either a parsimonius (SET_COVER) or a dynamic programming optimization approach. This stage takes into account constraints derived from mate pairs and spliced alignments and, optionally, knowledge about gene structure extracted from known annotation or alignments of cDNA sequences.

(Genome-guided assemblers) (Transcriptome assemblers)
Cufflinks Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols.

(Genome-guided assemblers) (Transcriptome assemblers)
iReckon iReckon is an algorithm for the simultaneous isoform reconstruction and abundance estimation. In addition to modelling novel isoforms, multi-mapped reads and read duplicates, this method takes into account the possible presence of unspliced pre-mRNA and intron retention. iReckon only requires a set of transcription start and end sites, but can use known full isoforms to improve sensitivity. Starting from the set of nearly all possible isoforms, iReckon uses a regularized EM algorithm to determine those actually present in the sequenced sample, together with their abundances. iReckon is multi-threaded to increase efficiency in all its time consuming steps.

(Genome-guided assemblers) (Transcriptome assemblers)
IsoInfer IsoInfer is a C/C++ program to infer isoforms based on short RNA-Seq (single-end and paired-end) reads, exon-intron boundary and TSS/PAS information.

(Genome-guided assemblers) (Transcriptome assemblers)
IsoLasso IsoLasso is an algorithm to assemble transcripts and estimate their expression levels from RNA-Seq reads.

(Genome-guided assemblers) (Transcriptome assemblers)
Flipflop FlipFlop implements a fast method for de novo transcript discovery and abundance estimation from RNA-Seq data. It differs from Cufflinks by simultaneously performing the identification and quantitation tasks using a convex penalized maximum likelihood approach, which leads to improved precision/recall.

(Genome-guided assemblers) (Transcriptome assemblers)
GIIRA GIIRA is a gene prediction method that identifies potential coding regions exclusively based on the mapping of reads from an RNA-Seq experiment. It was foremost designed for prokaryotic gene prediction and is able to resolve genes within the expressed region of an operon. However, it is also applicable to eukaryotes and predicts exon intron structures as well as alternative isoforms.

(Genome-guided assemblers) (Transcriptome assemblers)
MITIE Simultaneous RNA-Seq-based Transcript Identification and Quantification in Multiple Samples.

(Genome-guided assemblers) (Transcriptome assemblers)
RNAeXpress RNA-eXpress was designed as a user friendly solution to extract and annotate biologically important transcripts from next generation RNA sequencing data. This approach complements existing gene annotation databases by ensuring all transcripts present in the sample are considered for further analysis.

(Genome-guided assemblers) (Transcriptome assemblers)
Scripture Scripture is a method for transcriptome reconstruction that relies solely on RNA-Seq reads and an assembled genome to build a transcriptome ab initio. The statistical methods to estimate read coverage significance are also applicable to other sequencing data. Scripture also has modules for ChIP-Seq peak calling.

(Genome-guided assemblers) (Transcriptome assemblers)
SLIDE Sparse Linear modeling of RNA-Seq data for Isoform Discovery and abundance Estimation.

(Genome-guided assemblers) (Transcriptome assemblers)
Strawberry A program for fast and accurate genome-guided transcripts reconstruction and quantification from paired-end RNA-seq.

(Genome-guided assemblers) (Transcriptome assemblers)
StringTie StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Its input can include not only the alignments of raw reads used by other transcript assemblers, but also alignments longer sequences that have been assembled from those reads. To identify differentially expressed genes between experiments, StringTie's output can be processed either by the Cuffdiff or Ballgown programs.

(Genome-guided assemblers) (Transcriptome assemblers)
TransComb a genome-guided transcriptome assembly via combing junctions in splicing graphs.

(Genome-guided assemblers) (Transcriptome assemblers)
Traph A tool for transcript identification and quantification with RNA-Seq.

(Genome-guided assemblers) (Transcriptome assemblers)
Tiling Assembly for Annotation-independent Novel Gene Discovery.

(Genome-guided assemblers) (Transcriptome assemblers)
Bridger was developed at Shandong University, takes advantage of techniques employed in Cufflinks to overcome limitations of the existing de novo assemblers.

(Genome-independent (de novo) assemblers) (Transcriptome assemblers)
CLC de novo assembly algorithm of CLC Genomics Workbench.

(Genome-independent (de novo) assemblers) (Transcriptome assemblers)
KISSPLICE is a software that enables to analyse RNA-seq data with or without a reference genome. It is an exact local transcriptome assembler that allows to identify SNPs, indels and alternative splicing events. It can deal with an arbitrary number of biological conditions, and will quantify each variant in each condition.

(Genome-independent (de novo) assemblers) (Transcriptome assemblers)
Oases De novo transcriptome assembler for very short reads.

(Genome-independent (de novo) assemblers) (Transcriptome assemblers)
rnaSPAdes

(Genome-independent (de novo) assemblers) (Transcriptome assemblers)
Rnnotator an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads.

(Genome-independent (de novo) assemblers) (Transcriptome assemblers)
SAT-Assembler

(Genome-independent (de novo) assemblers) (Transcriptome assemblers)
SOAPdenovo-Trans

(Genome-independent (de novo) assemblers) (Transcriptome assemblers)
Scaffolding Translation Mapping

(Genome-independent (de novo) assemblers) (Transcriptome assemblers)
Trans-ABySS

(Genome-independent (de novo) assemblers) (Transcriptome assemblers)
T-IDBA

(Genome-independent (de novo) assemblers) (Transcriptome assemblers)
Trinity a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads.

(Genome-independent (de novo) assemblers) (Transcriptome assemblers)
Velvet

(Genome-independent (de novo) assemblers) (Transcriptome assemblers)
TransLiG

(Genome-independent (de novo) assemblers) (Transcriptome assemblers)
Busco provides quantitative measures for the assessment of genome assembly, gene set, and transcriptome completeness, based on evolutionarily-informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB tool.

(Assembly evaluation tools) (Transcriptome assemblers)
Detonate DETONATE (DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation) consists of two component packages, RSEM-EVAL and REF-EVAL. Both packages are mainly intended to be used to evaluate de novo transcriptome assemblies, although REF-EVAL can be used to compare sets of any kinds of genomic sequences.

(Assembly evaluation tools) (Transcriptome assemblers)
rnaQUAST Quality Assessment Tool for Transcriptome Assemblies.

(Assembly evaluation tools) (Transcriptome assemblers)
TransRate Transrate is software for de-novo transcriptome assembly quality analysis. It examines your assembly in detail and compares it to experimental evidence such as the sequencing reads, reporting quality scores for contigs and assemblies. This allows you to choose between assemblers and parameters, filter out the bad contigs from an assembly, and help decide when to stop trying to improve the assembly.

(Assembly evaluation tools) (Transcriptome assemblers)
GeneNetWeaver is an open-source tool for in silico benchmark generation and performance profiling of network inference methods. (Co-expression networks)
WGCNA is an R package for weighted correlation network analysis. (Co-expression networks)
Pigengene is an R package that infers biological information from gene expression profiles. Based on a coexpression network, it computes eigengenes and effectively uses them as features to fit decision trees and Bayesian networks that are useful in diagnosis and prognosis. (Co-expression networks)
iSRAP a one-touch research tool for rapid profiling of small RNA-seq data. (miRNA prediction and analysis)
SPAR small RNA-seq, short total RNA-seq, miRNA-seq, single-cell small RNA-seq data processing, analysis, annotation, visualization, and comparison against reference ENCODE and DASHR datasets. (miRNA prediction and analysis)
miRDeep2 (miRNA prediction and analysis)
MIReNA (miRNA prediction and analysis)
miRExpress (miRNA prediction and analysis)
miR-PREFeR m (miRNA prediction and analysis)
miRDeep-P For plants (miRNA prediction and analysis)
miRDeep (miRNA prediction and analysis)
miRPlant (miRNA prediction and analysis)
MiRdup (miRNA prediction and analysis)
ShortStack An alignment and annotation suite intended for small RNA analysis in plants, noted for its focus on high-confidence annotations (miRNA prediction and analysis)
ABrowse a customizable next-generation genome browser framework. (Visualization tools)
Artemis Artemis is a free genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation. (Visualization tools)
Apollo Apollo is designed to support geographically dispersed researchers, and the work of a distributed community is coordinated through automatic synchronization: all edits in one client are instantly pushed to all other clients, allowing users to see annotation updates from collaborators in real-time during the editing process. (Visualization tools)
BamView BamView is a free interactive display of read alignments in BAM data files. It has been developed by the Pathogen Group at the Sanger Institute. (Visualization tools)
BrowserGenome: web-based RNA-seq data analysis and visualization. (Visualization tools)
Degust An interactive web tool for visualising Differential Gene Expression data. (Visualization tools)
DensityMap is a perl tool for the visualization of features density along chromosomes. (Visualization tools)
EagleView EagleView is an information-rich genome assembler viewer with data integration capability. EagleView can display a dozen different types of information including base qualities, machine specific trace signals, and genome feature annotations. (Visualization tools)
expvip-web a customisable RNA-seq data analysis and visualisation platform. (Visualization tools)
GBrowse (Visualization tools)
Integrated Genome Browser (Visualization tools)
Integrative Genomics Viewer (IGV) (Visualization tools)
GenomeView (Visualization tools)
MapView (Visualization tools)
MicroScope comprehensive genome analysis software suite for gene expression heatmaps. (Visualization tools)
ReadXplorer ReadXplorer is a freely available comprehensive exploration and evaluation tool for NGS data. It extracts and adds quantity and quality measures to each alignment in order to classify the mapped reads. This classification is then taken into account for the different data views and all supported automatic analysis functions. (Visualization tools)
RNASeqExpressionBrowser is a web-based tool which provides means for the search and visualization of RNA-seq expression data (e.g. based on sequence-information or domain annotations). It can generate detailed reports for selected genes including expression data and associated annotations. If needed, links to (publicly available) databases can be easily integrated. The RNASeqExpressionBrowser allows password protection and thereby access restriction to authorized users only. (Visualization tools)
Savant Savant is a next-generation genome browser designed for the latest generation of genome data. (Visualization tools)
Samscope (Visualization tools)
SeqMonk (Visualization tools)
Tablet TTablet is a lightweight, high-performance graphical viewer for next generation sequence assemblies and alignments. (Visualization tools)
Tbrowse- HTML5 Transcriptome Browser (Visualization tools)
TBro a transcriptome browser for de novo RNA-sequencing experiments. (Visualization tools)
Vespa (Visualization tools)
BioCyc Visualize RNA-seq data onto individual pathway diagrams, multi-pathway diagrams called pathway collages, and zoomable organism-specific metabolic map diagrams. Computes pathway enrichment. (Functional, network and pathway analysis tools)
BRANE Clust Biologically-Related Apriori Network Enhancement for Gene Regulatory Network Inference combined with clustering. (Functional, network and pathway analysis tools)
BRANE Cut Biologically-Related Apriori Network Enhancement with Graph cuts for Gene Regulatory Network Inference. (Functional, network and pathway analysis tools)
FunRichFunctional Enrichment analysis tool. (Functional, network and pathway analysis tools)
GAGE is applicable independent of sample sizes, experimental design, assay platforms, and other types of heterogeneity. This Biocondutor package also provides functions and data for pathway, GO and gene set analysis in general. (Functional, network and pathway analysis tools)
Gene Set Association Analysis for RNA-Seq GSAASeq are computational methods that assess the differential expression of a pathway/gene set between two biological states based on sequence count data. (Functional, network and pathway analysis tools)
GeneSCF a real-time based functional enrichment tool with support for multiple organisms. (Functional, network and pathway analysis tools)
GOexpress Visualise microarray and RNAseq data using gene ontology annotations. (Functional, network and pathway analysis tools)
GOSeq Gene Ontology analyser for RNA-seq and other length biased data. (Functional, network and pathway analysis tools)
GSAASEQSP A Toolset for Gene Set Association Analysis of RNA-Seq Data. (Functional, network and pathway analysis tools)
GSVA gene set variation analysis for microarray and RNA-Seq data. (Functional, network and pathway analysis tools)
Heat*Seq an interactive web tool for high-throughput sequencing experiment comparison with public data. (Functional, network and pathway analysis tools)
Ingenuity Systems (commercial) iReport & IPA (Functional, network and pathway analysis tools)
PathwaySeq Pathway analysis for RNA-Seq data using a score-based approach. (Functional, network and pathway analysis tools)
petal Co-expression network modelling in R. (Functional, network and pathway analysis tools)
ToPASeq: an R package for topology-based pathway analysis of microarray and RNA-Seq data. (Functional, network and pathway analysis tools)
RNA-Enrich A cut-off free functional enrichment testing method for RNA-seq with improved detection power. (Functional, network and pathway analysis tools)
TRAPID Rapid Analysis of Transcriptome Data. (Functional, network and pathway analysis tools)
T-REx RNA-seq expression analysis. (Functional, network and pathway analysis tools)
Frama From RNA-seq data to annotated mRNA assemblies. (Further annotation tools for RNA-Seq data)
HLAminer is a computational method for identifying HLA alleles directly from whole genome, exome and transcriptome shotgun sequence datasets. HLA allele predictions are derived by targeted assembly of shotgun sequence data and comparison to a database of reference allele sequences. This tool is developed in perl and it is available as console tool. (Further annotation tools for RNA-Seq data)
pasaPASA, acronym for Program to Assemble Spliced Alignments, is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maintain gene structure annotation consistent with the most recently available experimental sequence data. PASA also identifies and classifies all splicing variations supported by the transcript alignments. (Further annotation tools for RNA-Seq data)
seq2HLA is an annotation tool for obtaining an individual's HLA class I and II type and expression using standard NGS RNA-Seq data in fastq format. It comprises mapping RNA-Seq reads against a reference database of HLA alleles using bowtie, determining and reporting HLA type, confidence score and locus-specific expression level. This tool is developed in Python and R. It is available as console tool or Galaxy module. (Further annotation tools for RNA-Seq data)
Brain RNA-Seq An RNA-Seq transcriptome and splicing database of glia, neurons, and vascular cells of the cerebral cortex.

(Human related) (RNA-Seq databases)
FusionCancer a database of cancer fusion genes derived from RNA-seq data.

(Human related) (RNA-Seq databases)
Hipposeq a comprehensive RNA-seq database of gene expression in hippocampal principal neurons.

(Human related) (RNA-Seq databases)
Mitranscriptome is a systematic list of long poly-adenylated Human RNA transcripts based on RNA-Seq data from more than 6,500 samples associated with a variety of cancer and tissue types. The database contains detailed gene expression analysis of over 91,000 genes, most are uncharacterized long RNAs.

(Human related) (RNA-Seq databases)
RNA-Seq Atlas a reference database for gene expression profiling in normal tissue by next-generation sequencing.

(Human related) (RNA-Seq databases)
SRA The Sequence Read Archive (SRA) stores raw sequence data from "next-generation" sequencing technologies including 454, IonTorrent, Illumina, SOLiD, Helicos and Complete Genomics. In addition to raw sequence data, SRA now stores alignment information in the form of read placements on a reference sequence.

(Human related) (RNA-Seq databases)
DASHR A database of human small RNA genes and mature products derived from small RNA-seq data.

(Human related) (RNA-Seq databases)
Aedes-albopictus Aedes albopictus database.

(Single species' RNA-Seq databases) (RNA-Seq databases)
Arabidopsis thaliana TraVa the database of gene expression profiles in Arabidopsis thaliana based on RNA-seq analysis.

(Single species' RNA-Seq databases) (RNA-Seq databases)
Barley morexGenes- Barley RNA-seq Database.

(Single species' RNA-Seq databases) (RNA-Seq databases)
Chickpea Chickpea transcriptome database (CTDB) has been developed with the view to provide most comprehensive information about the chickpea transcriptome, the most relevant part of the genome".

(Single species' RNA-Seq databases) (RNA-Seq databases)
Chilo suppressalis ChiloDB : a genomic and transcriptome database for an important rice insect pest Chilo suppressalis.

(Single species' RNA-Seq databases) (RNA-Seq databases)
Fruit fly FlyAtlas 2 - Drosophila melanogaster RNA-seq database.

(Single species' RNA-Seq databases) (RNA-Seq databases)
Echinoderm EchinoDB – a repository of orthologous transcripts from echinoderms.

(Single species' RNA-Seq databases) (RNA-Seq databases)
Equine transcriptome (University of California, Davis).

(Single species' RNA-Seq databases) (RNA-Seq databases)
Escherichia coli Ecomics – an omics normalized database for Escherichia coli.

(Single species' RNA-Seq databases) (RNA-Seq databases)
Fish Phylofish.

(Single species' RNA-Seq databases) (RNA-Seq databases)
Ginger Ginger - Ginger transcriptome database.

(Single species' RNA-Seq databases) (RNA-Seq databases)
Lygodium japonicum Lygodium japonicum Transcriptome Database.

(Single species' RNA-Seq databases) (RNA-Seq databases)
Mammals Mammalian Transcriptomic Database.

(Single species' RNA-Seq databases) (RNA-Seq databases)
Oyster (Pacific) GigaTon: an extensive publicly searchable database providing a new reference transcriptome in the pacific oyster Crassostrea gigas.

(Single species' RNA-Seq databases) (RNA-Seq databases)
Mouse and Human PanglaoDB: A gene expression database for exploration and meta-analysis of single cell sequencing data.

(Single species' RNA-Seq databases) (RNA-Seq databases)
Mangrove Mangrove Transcriptome Database.

(Single species' RNA-Seq databases) (RNA-Seq databases)
Krill (Antarctic) KrillDB: a de novo Transcriptome Database for the Antarctic Krill.

(Single species' RNA-Seq databases) (RNA-Seq databases)
Mouse RNASeqMetaDB: a database and web server for navigating metadata of publicly available mouse RNA-Seq data sets.

(Single species' RNA-Seq databases) (RNA-Seq databases)
Rubus Rubus GDR RefTrans V1 - GDR Rubus RefTrans combines published RNA-Seq and EST data sets to create a reference transcriptome (RefTrans) for rubus and provides putative gene function identified by homology to known proteins.

(Single species' RNA-Seq databases) (RNA-Seq databases)
Sorghum MOROKOSHI Sorghum transcriptome database. RIKEN full-length cDNA clone and RNA-Seq data in Sorghum bicolor.

(Single species' RNA-Seq databases) (RNA-Seq databases)
S. purpuratus S. purpuratus - Developmental Transcriptomes of S. purpuratus

(Single species' RNA-Seq databases) (RNA-Seq databases)
S. cerevisiae YeastMine transcriptome database.

(Single species' RNA-Seq databases) (RNA-Seq databases)
Wheat WheatExp – an RNA-seq expression database for polyploid wheat.

(Single species' RNA-Seq databases) (RNA-Seq databases)

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About This Tool

RNA-seq, or transcriptome sequencing, is the high-throughput sequencing of mRNA, small RNA, and NONcoding RNA, or some of them, to reflect their level of expression. A transcriptome is a collection of all transcripts produced by a particular species or cell type.

Transcriptome studies can study the function and structure of genes at a holistic level, and reveal the molecular mechanisms underlying specific biological processes and disease processes, it has been widely used in basic research, clinical diagnosis and drug research and development. The 509 entries generated by the random tool record various areas of application of the RNA-seq technology, including design, quality control, other application equipment, etc.

Click the "Display All Items" button and you will get a list of RNA-Seq bioinformatics tools.

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List of RNA-Seq Bioinformatics Tools (509 items)report

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