Release 1.5.0-p2, 14 Apr 2016
subread-align and subjunc
- Fix a bug in processing long header lines in SAM/BAM files.
- Depreciated the '-S < ff:fr:rf >' option.
- The '< input file >.featureCounts' files (generated when '-R' is specified) are saved to the same directory as the file < output_file >.
- Fixed a bug related to reporting of reads mapping out of the chromosomal boundary.
- Make sure no zero operations (eg '0M') are included in reported CIGAR strings.
- Fixed a bug in soft-clipping read bases.
- Improved screen output.
Release 1.5.0-p1, 18 Dec 2015
featureCounts can process long reads (up to 250kb long). It can also process reads that contain long extra fields.
Report counts for exon-exon junctions by featureCounts ('-J' option).
Improved parsing of gzipped fastq files in Subread and Subjunc aligners.
Release 1.5.0, 29 Oct 2015
subread-align and subjunc
- Improved speed of re-sorting paired-end reads. It now takes only about 30 seconds to re-sort 30 million read pairs.
- A utility program `repair' to provided to allow pre-sorting of pair-end BAM/SAM files.
- New parameter '--type' for sequencing-type-specific mapping optimization.
- New parameter '--sv' for detection of structural variant breakpoints.
- New parameter '--complexIndels' for detection of complex indels.
- Improved mapping of paired-end reads via a new formula that uses weighted votes (more weight is given to properly mapped reads).
- Improved detection of multi-mapping reads by considering locations that receive second highest votes.
- When gzipped fastq input is provided, reads will be directly extracted from the gzip-compressed file and no temporary files will be generated.
- Default output format is set to BAM.
- Default threshold for removing un-informative subreads from index is changed to 100 to allow more candidate mapping locations to be considered.
Release 1.4.6-p5, 4 Sept 2015
Added '-S' option to featureCounts to specify the orientation of paired-end reads.
Added '--minOverlap' and '--largestOverlap' options to featureCounts.
Fixed a CIGAR reporting bug in Subjunc when '--allJunctions' option is turned on (in rare cases CIGAR may contain an incorrect large N section).
Release 1.4.6-p4, 25 June 2015
Fixed a bug in featureCounts for counting reads (not read pairs) in stranded paired-end sequencing data. Counting read pairs is not affected by this bug.
Release 1.4.6-p3, 18 May 2015
Added an argument "--donotsort" to featureCounts to allow users to turn off the read sorting procedure.
Show details of read pairs that were not properly paired in featureCounts screen output.
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:
Transcriptional profiling of mouse B cell terminal differentiation defines a signature for antibody-secreting plasma cells
Release 1.4.6-p2, 24 March 2015
Added a new parameter for subread-align and subjunc programs: --minDistanceBetweenVariants. This parameter specifies the minimum allowed distance between two neighboring genomic variants within the same read.
Release 1.4.6-p1, 12 Feb 2015
Distance between two neighboring genomic variants is allowed to be as small as 1bp (it was 16bp).
Fix a bug that sometimes caused randomness in multi-threaded running of Subjunc program.
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
The default number of maximum allowed mismatches in each reported alignment is changed to 3.
The minimun fraction of consensus subreads out of all extracted subreads, required for detecting candidate mapping locations, is changed to 0.3 in subjunc for the mapping of exonic reads (reads falling within exons).
Better support for the mapping of micro RNA sequencing (miRNA-seq) reads. A full index with no gaps included can now be built to allow miRNA-seq reads to be mapped in the highest possible resolution. A new section is added to the User Guides to describe how to map miRNA-seq reads using Subread.
Download and Installation
Latest version 1.5.0-p2
All the versions
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
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
Read count tables for Pickrell dataset and Montgomery dataset, both published in Nature in 2010.
Read count table for TCGA data.
Read count data from SEQC/MAQC III study.
Bioconductor R package Rsubread
Bioconductor R package seqc
Dr. Wei Shi (shi at wehi dot edu dot au) or
Dr. Yang Liao (liao at wehi dot edu dot au)