Subread

Category

Bioinformatics, Aligner

Description

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
	1.5.0

Please note that this page refers to installations from the old software stack. There are two software stacks on Euler. Newer versions of software are found in the new software stack.

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

Please note that this page refers to installations from the old software stack. There are two software stacks on Euler. Newer versions of software are found in the new software stack.

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

GPLv3

Links

http://bioinf.wehi.edu.au/subread

http://subread.sourceforge.net