DOI: 10.18129/B9.bioc.Rsubread    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see Rsubread.

Subread Sequence Alignment and Counting for R

Bioconductor version: 3.9

Alignment, quantification and analysis of second and third generation sequencing data. Includes functionality for read mapping, read counting, SNP calling, structural variant detection and gene fusion discovery. Can be applied to all major sequencing techologies and to both short and long sequence reads.

Author: Wei Shi, Yang Liao and Gordon K Smyth with contributions from Jenny Dai

Maintainer: Wei Shi <shi at>, Yang Liao <liao at> and Gordon K Smyth <smyth at>

Citation (from within R, enter citation("Rsubread")):


To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



PDF R Script Rsubread Vignette
PDF SubreadUsersGuide.pdf
PDF   Reference Manual
Text   NEWS


biocViews Alignment, ChIPSeq, GeneExpression, GeneFusionDetection, GeneRegulation, GeneticVariability, Genetics, GenomeAnnotation, ImmunoOncology, IndelDetection, MultipleSequenceAlignment, Preprocessing, QualityControl, RNASeq, SNP, SequenceMatching, Sequencing, Software, VariantAnnotation, VariantDetection
Version 1.34.7
In Bioconductor since BioC 2.8 (R-2.13) (8.5 years)
License GPL-3
Imports grDevices, stats, utils
Depends On Me ExCluster, samExploreR
Imports Me dupRadar
Suggests Me icetea, scPipe, scruff, singleCellTK
Links To Me
Build Report  

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Follow Installation instructions to use this package in your R session.

Source Package Rsubread_1.34.7.tar.gz
Windows Binary (32- & 64-bit)
Mac OS X 10.11 (El Capitan) Rsubread_1.34.7.tgz
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