RNA sequencing data analysis bioinformatics software tools

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 need to know the RNA sequence…

RNA-seq analysis steps

Preprocessing & quality control

Data analysis

Annotation & interpretation

File, data & workflows

RNA-seq analysis workflow

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RNA-seq analysis workflow schema

Most recent bioinformatics tools

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ISEA
Desktop

ISEA Iterative Seed-Extension Algorithm

Provides an iterative seed-extension algorithm for de novo assembly. ISEA…

Provides an iterative seed-extension algorithm for de novo assembly. ISEA comports five steps: (i) preprocessing, (ii) graph and seed building, (iii) contig extension, (iv) merging and (v)…

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PORT
Desktop

PORT Pipeline of RNA-Seq Transformations

Allows users to work on normalization or quantification of RNA-seq. PORT…

Allows users to work on normalization or quantification of RNA-seq. PORT enables to realize two types of normalization: (1) exon-intron-junction normalization and (2) gene normalization.

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SOAPaligner
Desktop

SOAPaligner Short Oligonucleotide Analysis Package

Enables ultrafast and memory-efficient alignment of massive short sequencing…

Enables ultrafast and memory-efficient alignment of massive short sequencing reads. SOAPaligner permits users to index the reference and perform reads alignment. It can tolerate as low as 60 per cent…

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DeDup
Desktop

DeDup

Removes duplicate merged reads on single end data. DeDup can be applied to…

Removes duplicate merged reads on single end data. DeDup can be applied to forward, reverse and merged reads. It retains a single read for a given genomic position and read direction to deduplicate…

Most popular analytical software

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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…

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Bowtie
Desktop

Bowtie

A short read aligner that aligns short DNA sequences (reads) to the human…

A short read aligner that 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 Burrows-Wheeler index to keep its…

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Trimmomatic
Desktop

Trimmomatic

Performs a variety of useful trimming tasks for illumina paired-end and single…

Performs a variety of useful trimming tasks for illumina paired-end and single ended data.

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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…

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
    Centre François Baclesse

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