Subread
Description
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: a general-purpose read aligner which can align both genomic DNA-seq and RNA-seq reads. It can also be used to discover genomic mutations including short indels and structural variants.
- Subjunc: a read aligner developed for aligning RNA-seq reads and for the detection of exon-exon junctions. Gene fusion events can be detected as well.
- featureCounts: a software program developed for counting reads to genomic features such as genes, exons, promoters and genomic bins.
- exactSNP: a SNP caller that discovers SNPs by testing signals against local background noises.
License
Subread is a free open source software under GNU GENERAL PUBLIC LICENSE 3
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of subread and load default version of subread as
module avail subread/ # list available modules module load subread # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail subread
and choose explicit version you want to use. Then run as:
subread-buildindex subread-align --help
Documentation
- Manual PDF.