The Subread package comprises a suite of software programs for processing next-gen sequencing read data including:
- Subread: an accurate and efficient aligner for mapping both genomic DNA-seq reads and RNA-seq reads (for the purpose of expression analysis).
- Subjunc: an RNA-seq aligner suitable for all purposes of RNA-seq analyses.
- featureCounts: a highly efficient and accurate read summarization program.
- exactSNP: a SNP caller that discovers SNPs by testing signals against local background noises.
These programs were also implemented in Bioconductor R package Rsubread.
The Subread-featureCounts-limma/voom pipeline was successfully used in a large-scale RNA-seq study for defining a signature for mouse antibody-secreting plasma cells. The study was published in Nature Immunology in April 2015:
Release 1.4.6-p2, 24 March 2015
Release 1.4.6-p1, 12 Feb 2015
The Subread-featureCounts-limma/voom pipeline has been found to be one of the best-performing pipelines for the analyses of RNA-seq data by the SEQC/MAQC III Consortium. This study was published in the 2014 September issue of Nature Biotechnology -- A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium
Release 1.4.6, 15 Oct 2014
Release 1.4.5-p1, 7 July 2014
Release 1.4.5, 12 June 2014New options in featureCounts:
--readExtension5 <int> Reads are extended upstream by <int> bases from their 5' end. --readExtension3 <int> Reads are extended downstream by <int> bases from their 3' end. --read2pos <5:3> The read is reduced to its 5' most base or 3' most base. Read summarization is then performed based on the single base position which the read is reduced to. --minReadOverlap <int> Specify the minimum number of overlapped bases required for assigning a read to a feature. 1 by default. Negative values are permitted, indicating a gap being allowed between a read and a feature. --countSplitAlignmentsOnly If specified, only split alignments (CIGAR strings containing letter 'N') will be counted. Example split alignments include exon-spanning reads in RNA-seq data. --ignoreDup If specified, reads marked as duplicates are not counted. Duplicate reads are identified using FLAG Ox400. A new option in subread-align/sbujunc: -M <int> Specify the maximum number of mismatched bases allowed in the alignment. 10 by default. Other changes:
Download and Installation
Tutorials and Users Guide
Scientific publications citing our methods
Dr. Wei Shi (shi at wehi dot edu dot au) or