subread 1.5.3

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.

Accessing the software

To load the module:

$ module load apps/subread/1.5.3

An example command to include in your job script:

subread-align -i <my_index> -r <reads.txt> -t 0 -o <subread_results.bam>

Where brackets <...> indicate positional arguments to subread-align.

Useful usage information can be found at ${SUBREAD_ROOT}/README.txt

Accessing Previous Versions

Wherever possible, previous versions of this application will be retained for continuity, especially for research projects that require a consistent version of the software throughout the project. Such versions, however, may be unsupported by IT Services or the applications vendor, and may be withdrawn at short or no notice if they can no longer run on the cluster - for example, essential operating system upgrades may be incompatible with old versions.

At present there are no previous versions of this application on the BlueBEAR service.

Known Problems & Limitations


Other Information

The Support Level for this application is An.

Visit the subread website for more information regarding this application.

Last modified: 14 August 2017