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Bioinformatics, Aligner


Subread is 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.

Available versions (Euler, old software stack)

Legacy versions Supported versions New versions

Environment modules (Euler, old software stack)

Version Module load command Additional modules loaded automatically
1.5.0 module load gcc/4.8.2 subread/1.5.0

How to submit a job

You can submit a subread job in batch mode with the following command:
bsub [LSF options] "[executable] [options]"

where you need to replace [LSF options] with LSF parameters for the resource requirements of the job. Please find a documentation about the parameters of bsub on the wiki page about the batch system.

Here [executable] is one of the following executables:

exactSNP, featureCounts, subindel, subjunc, subread-align, subread-buildindex
and [options] needs to be replaced by subread command line options.

License information