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

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ANGSD
Desktop

ANGSD

Analyses next generation sequencing (NGS) data. ANGSD can handle a number of…

Analyses next generation sequencing (NGS) data. ANGSD can handle a number of different input types from mapped reads to imputed genotype probabilities. Most methods take genotype uncertainty into…

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Manananggal
Desktop

Manananggal

Uses to detect alternative splicing events (ASEs). This application written in…

Uses to detect alternative splicing events (ASEs). This application written in Java can, through a web application, scans RNAseq data to identify them, and Manananggal can also be launched as a…

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savR
Desktop

savR

Parses Illumina Sequence Analysis Viewer (SAV) files, access data, and generate…

Parses Illumina Sequence Analysis Viewer (SAV) files, access data, and generate QC plots. SavR offers functions to generate a folder of images that approximates the format of the folder that was…

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Threshold-seq
Desktop

Threshold-seq

Determines thresholds in deep-sequencing datasets of short RNA transcripts.…

Determines thresholds in deep-sequencing datasets of short RNA transcripts. Threshold-seq addresses the critical question of how many reads need to support a short RNA molecule in a given dataset…

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

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