The Subread package (original) (raw)

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:

Release 2.0.7, 17 October 2024

Release 2.0.6, 10 May 2023

Fixed a bug in featureCounts when counting reads supporting each exon-exon junction in long-read data.

Release 2.0.5, 17 April 2023

Release 2.0.4, 27 February 2023

'--fraction' parameter now works with '--largestOverlap' parameter in featureCounts.
Value provided to '--fracOverlap' parameter in featureCounts is now precisely applied for read filtering.
'-J' parameter in featureCounts now considers all the reads in the input for junction counting.

Release 2.0.3, 15 July 2021

Release 2.0.2, 29 March 2021

New parameter '--countReadPairs' is added to featureCounts to explicitly specify that read pairs will be counted, and the '-p' option in featureCounts now only specifies if the input reads are paired end (it also implied that counting of read pairs would be performed in previous versions).

Release 2.0.1, 13 May 2020

Release 2.0.0, 4 Sept 2019 -- We finally ported Subread package to Windows!

Release 1.6.5, 18 Jul 2019

Reduce the amount of computer memory used by subread-buildindex program to build an index.
Use the first 1000 mapped read pairs to estimate the template length and use this information to improve the mapping of paired end reads.
Improve the detection and reporting of indels that are present in repetitive genomic regions.
Input BAM/SAM files to featureCounts program are allowed to contain both single-end and paired-end reads.
flattenGTF can combine overlapping exons to form a single large exon encompassing all the overlapping exons, or chop them into non-overlapping bins.
Algorithm improvement for exactSNP program.

Release 1.6.4, 14 Mar 2019

New options in featureCounts: readShiftType and readShiftSize.
The fasta file(s) provided to subread-buildindex is allowed to be in gzipped format.
removeDup utility program supports BAM input and output.
Improved checking on file read and write operations.

Release 1.6.3, 9 Oct 2018

Fixed a bug in subread-align and subjunc that may cause incorrect reporting of mapping result when a read is mapped out of chromosome boundary.
Fixed a bug in featureCounts that may cause incorrect counting of reads when '--byReadGroup' is specified and unmapped reads are not included in the BAM input.
Limit on the size of header in the SAM input is removed from featureCounts.
Depreciated the coverageCount utility function.

Release 1.6.2, 15 May 2018

featureCounts
New parameter '--extraAttributes': allow extra attributes to be included in the counting output.
Stranded/unstranded counting can be applied to each individual library ('-s' option).
Improve the speed of featureCounts in processing BAM files generated by some tools which produce reads that are stored in more than one BAM block.
subread-align and subjunc
New parameter '--sortReadsByCoordinates': output location-sorted reads in BAM output.
New parameter '--keepReadOrder': reads in the mapping output are kept in the same order as that in the input.
New function 'flattenGTF': flatten features included in a GTF/GFF annotation and output modified annotation to a SAF format annotation.

Release 1.6.1, 23 March 2018

featureCounts
Add two new parameters: nonOverlap and nonOverlapFeature.
subread-align
Breakpoint data generated with the '--sv' option are written into a VCF-format file.
Subread-align, subjunc, featureCounts and exactSNP
Annotation file can be provided as a gzipped file.

Release 1.6.0, 14 Nov 2017

sublong
Release of Sublong: a seed-and-vote aligner for mapping long reads such as Nanopore and PacBio reads.
featureCounts
New parameter 'fracOverlapFeature' for checking fraction of overlapping bases in a feature.
For the counting of reads in read groups, order of read group columns in counting output is determined by the order of read group names appearing in the BAM/SAM header.

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