RNA sequencing data analysis bioinformatics software tools

RNA-seq analysis steps

Preprocessing & quality control

Data analysis

Annotation & interpretation

File, data & workflows

RNA-seq analysis workflow

Click the icons of the schema to view tools

RNA-seq analysis workflow schema
RNA sequencing (RNA-seq) also known as whole transcriptome shotgun sequencing (WTSS) is the next-generation sequencing technology to study the transcriptome. It could be used as an alternative to microarrays for gene expression analysis, without the…

RNA sequencing data analysis bioinformatics software tools

Most Recent Tools

G T A T C G C T A
RNA-seq 2G
Web

RNA-seq 2G

Uses read count data from RNA-seq or similar data matrix as input and generates…

Uses read count data from RNA-seq or similar data matrix as input and generates test statistics in consistent format as output. RNA-seq 2G is a web portal with over 25 statistical methods that…

G T A T C G C T A
tcgsaseq
Desktop

tcgsaseq

Applies to virtually all RNA-seq study designs, including traditional…

Applies to virtually all RNA-seq study designs, including traditional case-control and more complex studies. tcgsaseq is a principled, model-free and efficient top-down method for detecting…

G T A T C G C T A
Scallop
Desktop

Scallop

Enables accurate identification of multi-exon transcripts and lowly expressed…

Enables accurate identification of multi-exon transcripts and lowly expressed transcripts. Scallop is an accurate reference-based transcript assembler. The software uses a novel algorithm to…

G T A T C G C T A
CAT
Desktop

CAT Cross-species Alignment Tool

Aligns mRNA sequences to mammalian-sized genomes. CAT is designed to be a…

Aligns mRNA sequences to mammalian-sized genomes. CAT is designed to be a cross-species cDNA-to-genome alignment software. This algorithm was developed to combine the specificity of the intra-species…

Most Popular Tools

G T A T C G C T A
SAMtools
Desktop

SAMtools

A suite of programs for interacting with high-throughput sequencing data. It…

A suite of programs for interacting with high-throughput sequencing data. It can manipulate alignments in the SAM/BAM/CRAM formats : reading, writing, editing, indexing, viewing and converting…

G T A T C G C T A
Bowtie
Desktop

Bowtie

An ultrafast, memory-efficient short read aligner. It aligns short DNA…

An ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a…

G T A T C G C T A
AlienTrimmer
Desktop

AlienTrimmer

Detects and removes multiple alien sequences in both ends of sequence reads.…

Detects and removes multiple alien sequences in both ends of sequence reads. Based on the decomposition of specified alien nucleotide sequences into k-mers, AlienTrimmer is able to determine whether…

G T A T C G C T A
Trim Galore!
Desktop

Trim Galore!

A wrapper tool around Cutadapt and FastQC to consistently apply quality and…

A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation…

Curators for RNA-seq analysis

  • Rekin's Janky's avatar image
    Rekin's Janky
    Laboratory of Computational…
  • Bogdan Mirauta's avatar image
    Bogdan Mirauta
    Laboratory of Computational and…
  • Mikhail Shugay's avatar image
    Mikhail Shugay
    Genomics of Adaptive Immunity Lab,…
  • Abdoulaye Baniré Diallo's avatar image
    Abdoulaye Baniré Diallo
    Department of Computer Sciences,…
  • Antoine ROUSSELIN's avatar image Antoine ROUSSELIN's country flag
    Antoine ROUSSELIN
    Centra François Baclesse

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.