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: an accurate and efficient aligner for mapping both genomic DNA-seq reads and RNA-seq reads (for the purpose of expression analysis).
• Subjunc: an RNA-seq aligner suitable for all purposes of RNA-seq analyses.
• featureCounts: a highly efficient and accurate read summarization program.
• exactSNP: a SNP caller that discovers SNPs by testing signals against local background noises.

Subread can be run multi-threaded using -T flag on biowulf. See example below.

References:

• https://www.ncbi.nlm.nih.gov/pubmed/23558742
• http://www.ncbi.nlm.nih.gov/pubmed/24227677

• http://subread.sourceforge.net/

• Module Name: subread (see the modules page for more information)
• Subread can be run multi-threaded using -T flag on biowulf. See example below.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load subread
[user@cn3144 ~]$ cd /data/$USER/dir
[user@cn3144 ~]$ subread-align -i indexfile -r inputfile -o outputfile

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. subread.sh). For example:

#!/bin/bash
set -e
module load subread
cd /data/$USER/dir
subread-align -i indexfile -r inputfile -o outputfile

Submit this job using the Slurm sbatch command.

$ sbatch subread.sh

To run multi-threaded subread on biowulf:

#!/bin/bash

module load subread
cd /data/$USER/
subread-align -T $SLURM_CPUS_PER_TASK -i indexfile -r inputfile -o output

Submit the script:

$ sbatch --cpus-per-task=4 jobscript

--cpus-per-task: allocate 4 cpus. This number will be assigned to $SLURM_CPUS_PER_TASK automatically

For more memory requirement (default 4gb), use --mem flag:

$ sbatch --cpus-per-task=4 --mem=10g jobscript

Create a swarmfile (e.g. subread.swarm). For example:

cd dir1;subread-align -i indexfile -r inputfile -o outputfile
cd dir2;subread-align -i indexfile -r inputfile -o outputfile
cd dir3;subread-align -i indexfile -r inputfile -o outputfile
cd dir4;subread-align -i indexfile -r inputfile -o outputfile

Submit this job using the swarm command.

swarm -f subread.swarm [-g #] [-t #] --module subread