Subread

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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

Homepage

Subread home page