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.

Availability

Version:

  • 1.5.2 (modul subread-1.5.2)

Use

Example of module initialization and run:

module add subread-1.5.2
subread-buildindex
subread-align --help

Documentation

Licence

Subread is a free open source software under GNU GENERAL PUBLIC LICENSE 3

Program manager

meta@cesnet.cz

Homepage

Subread home page