The Subread package: a tool kit for processing next-gen sequencing data

The Subread package is developed in The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia. It consists of a suite of programs for processing next-gen sequencing data.

Functions

Below are some of the functions provided by this package:

Subread aligner: a general-purpose read aligner. 
Subjunc aligner: detecting exon-exon junctions and mapping RNA-seq reads.
featureCounts: counting mapped reads for genomic features.
exactSNP: a SNP caller that discovers SNPs by testing signals against local background noises.

Download and installation

Installation from a binary distribution

This is the easiest way to install the Subread package onto your computer. Download a Subread binary distribution that suits your oprating system from SourceForge website. The operating systems currently being supported include multiple variants of Linux (Debian, Ubuntu, Fedora and Cent OS) and Mac OS X. Both 64-bit and 32-bit machines are supported. The executables can be found in the bin diretory of the binary packages.

To install Subread package for other operating systems such as FreeBSD and Solaris, you will have to install them for the source.

Installation from the source

Download the Subread source package from SourceForge website to your local directory. Type the following command to uncompress it:

tar zxvf subread-1.x.x.tar.gz
Enter the src subdirectory under the home directory of the package and then issue the following command to build it on a Linux/unix computer:
make -f Makefile.Linux
To build it on a Mac OS X computer, issue the following command:
make -f Makefile.MacOS
To build it on a FreeBSD computer, issue the following command:
make -f Makefile.FreeBSD
To build it on a Oracle Solaris or OpenSolaris computer, issue the following command:
make -f Makefile.SunOS

A new subdirectory called bin will be created under the home directory of the package, and the executables generated from the build will be saved to that subdirectory. To enable easy access to these executables, you may copy them to a system directory such as /usr/bin or add the path to them to your search path (your search path is usually stored in environment variable PATH)

Citation

If you use the Subread or Subjunc aligners, please cite:

Liao Y, Smyth GK and Shi W (2013). The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Research, 41(10):e108

If you use the featureCounts program, please cite:

Liao Y, Smyth GK and Shi W (2014). featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics, 30(7):923-30.

Users Guide

The Users Guide (0.5MB) provides a comprehensive description to this software package.

Get help

The best way to get help is to send your questions to the SEQanswers mailing list or the Bioconductor mailing list. Alternatively, you may directly contact Dr. Wei Shi (shi at wehi dot edu dot au).

Scientific publications citing Subread and featureCounts

Publications that cite Subread/Subjunc aligners

Publications that cite featureCounts

Links

Subread: A superfast and accurate read aligner.

Subjunc: Detecting exon-exon junctions and mapping RNA-seq reads.

featureCounts: Summarizing reads to genomic features.

exactSNP: a SNP caller that discovers SNPs by testing signals against local background noises.

Rsubread: a Bioconductor R implementation of the Subread package.

A case study for analyzing RNA-seq data: Using Bioconductor packages Rsubread and Limma to perform a complete analysis for RNA-seq data.