subread

Overview

Subread is a a tool kit for processing next-gen sequencing data.

Version 2.0.0 is installed on the CSF3. It was compiled with Intel Compilers 18 (using -msse2 -axSSE4.2,AVX,CORE-AVX2,CORE-AVX512)

Restrictions on use

This software is open-source so all CSF users may use it.

If you use the Subread or Subjunc aligners, please cite:
Liao Y, Smyth GK and Shi W (2013). The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Research, 41(10):e108

If you use the featureCounts program, please cite:
Liao Y, Smyth GK and Shi W (2014). featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics, 30(7):923-30.

Set up procedure

For single (up to 32 core)  jobs:

module load apps/intel-18.0/subread/2.0.0

Running the application

• • Please do not run subread on the login node.
  • All Jobs should be submitted to the compute nodes via batch.
  • The $NSLOTS in the examples is important as it ensures correct utilisation of resources.

Parallel batch job submission – up to 32 cores on a (single compute node)

Make sure you have the modulefile loaded then create a batch submission script, for example:

#!/bin/bash --login
#$ -cwd
#$ -V
#$ -pe smp.pe 5

module load apps/intel-18.0/subread/2.0.0

subread-align -T $NSLOTS -i my_index -r input.file -t 1 -o output.file

Submit the jobscript using:

qsub scriptname

where scriptname is the name of your jobscript.

Further info

• Subread website
• Users guide (pdf)

Updates

None.