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

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.


Release 1.4.5-p1, 7 July 2014
  • Fixed a bug for reporting unmapped reads in SAM output.

  • Release 1.4.5, 12 June 2014

    New 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:
  • NM tags are added into read mapping output.
  • Range of MAPQ values is changed to [0,60).
  • MAPQ values for Multiple-mapping reads are set to 0.
  • NCBI RefSeq gene annotations for hg19, mm10 and mm9 are added to the package, making it easier for performing read summarization.
  • Bug fixes.

  • ChangeLog history

    Download and Installation

  • Latest version v1.4.5-p1
  • All the versions
  • Installation instructions
  • Mailing lists

  • Subread Users Group
  • Tutorials and Users Guide

  • A short tutorial on Subread
  • A short tutorial on Subjunc
  • A short tutorial on featureCounts
  • A short tutorial on exactSNP
  • A case study for analyzing RNA-seq data
  • Users Guide
  • Publications

  • Liao Y, Smyth GK and Shi W. The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Research, 41(10):e108, 2013
  • Liao Y, Smyth GK and Shi W. featureCounts: an efficient general-purpose program for assigning sequence reads to genomic features. Bioinformatics, 30(7):923-30, 2014
  • Scientific publications citing our methods

  • Publications that cite Subread/Subjunc
  • Publications that cite featureCounts
  • Resources

  • Read count tables for published datasets
  • Links

  • Rsubread: a Bioconductor R package
  • WEHI Bioinformatics
  • Contact

    Dr. Wei Shi (shi at wehi dot edu dot au) or
    Dr. Yang Liao (liao at wehi dot edu dot au)