Rsubread package: high-performance read alignment, quantification and mutation discovery

Bioconductor version: Release (2.14)

This R package provides powerful and easy-to-use tools for analyzing next-gen sequencing read data. Functions of this package include quality assessment of sequence reads, read alignment, read summarization, exon-exon junction detection, fusion detection, detection of short and long indels, absolute expression calling and SNP calling. This package can be used to anlayze data generated from all major sequencing platforms such as Illumina GA/HiSeq/MiSeq, Roche GS-FLX, ABI SOLiD and LifeTech Ion PGM/Proton sequencers. It supports multiple operating systems incluidng Linux, Mac OS X, FreeBSD and Solaris.

Author: Wei Shi and Yang Liao with contributions from Jenny Zhiyin Dai and Timothy Triche, Jr.

Maintainer: Wei Shi <shi at>

To install this package, start R and enter:


To cite this package in a publication, start R and enter:



PDF R Script Rsubread Vignette
PDF   Reference Manual
Text   NEWS


biocViews Alignment, ChIPSeq, GeneExpression, GeneRegulation, GeneticVariability, Genetics, GenomeAnnotation, Preprocessing, QualityControl, RNASeq, SNP, SequenceMatching, Sequencing, Software
Version 1.14.0
In Bioconductor since BioC 2.8 (R-2.13)
License GPL-3
System Requirements
Depends On Me
Imports Me
Suggests Me

Package Downloads

Package Source Rsubread_1.14.0.tar.gz
Windows Binary
Mac OS X 10.6 (Snow Leopard) Rsubread_1.14.0.tgz
Mac OS X 10.9 (Mavericks)
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