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

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RNA-seq analysis workflow schema
In recent years, the continuing technical improvements and decreasing cost of next-generation sequencing technology have made RNA sequencing (RNA-seq) a popular choice for gene expression studies (Wang et al., 2009; Ozsolak and Milos, 2011). Such…

RNA sequencing data analysis bioinformatics software tools

Most Recent Tools

CLOUD
Informatics…
Desktop

Informatics for RNA-seq

Stores code and certain raw materials for a detailed RNA-seq tutorial.…

Stores code and certain raw materials for a detailed RNA-seq tutorial. Informatics for RNA-seq is an educational tutorial and working demonstration pipeline for RNA-seq analysis including an…

G T A T C G C T A
ARSDA
Desktop

ARSDA Analyzing RNA-Seq Data

Alleviates the problem associated with storage, transmission and analysis of…

Alleviates the problem associated with storage, transmission and analysis of high-throughput sequencing (HTS) data. ARSDA can take as input .SRA files or .fastq files of many gigabytes, build an…

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IntEREst
Desktop

IntEREst Intron Exon Retention Estimator

Performs intron-exon retention analysis on RNA-seq data. IntEREst facilitates…

Performs intron-exon retention analysis on RNA-seq data. IntEREst facilitates estimation and comparison of splicing efficiency of various transcripts across several samples. In particular, it can…

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Nanocorrect
Desktop

Nanocorrect

Improves the accuracy of our nanopore reads to around 97% after two rounds of…

Improves the accuracy of our nanopore reads to around 97% after two rounds of correction. Nanocorrect is a prototype nanopore correction pipeline. This pipeline is inspired by pbdagcon which used…

Most Popular Tools

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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

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…

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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…

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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 BanirĂ© Diallo's avatar image
    Abdoulaye Baniré Diallo
    Department of Computer Sciences,…

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