Subread¶
The Subread package comprises a suite of software programs for processing next-gen sequencing read data.
Subread is available as a module on Apocrita.
Usage¶
To run the default installed version of Subread, simply load the
subread module:
$ module load subread
$ subread-align
Version X.Y.Z
Usage:
./subread-align [options] -i <index_name> -r <input> -t <type> -o <output>
For full usage documentation, refer to the Subread Users Guide.
Example job¶
Serial job¶
Core Usage
Please set any arguments such as:
# number of CPU threads
-T <int> Number of CPU threads used, 1 by default.
to the value of ${NSLOTS} (number of cores requested by the job script),
to avoid overloading the compute nodes.
Here is an example job running on 2 cores and 4GB of memory:
#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 2
#$ -l h_rt=1:0:0
#$ -l h_vmem=2G
module load subread
# Genome indexing
# Build a base-space index (default). You can provide a list of FASTA files or
# a single FASTA file including all the reference sequences. The files can be
# gzipped.
subread-buildindex -o my index chr1.fa chr2.fa ...
# Genome alignment
# Map single-end genomic DNA sequencing reads matching threads to ${NSLOTS}
# (only uniquely mapped reads are reported):
subread-align -t 1 \
-T ${NSLOTS} \
-i my index \
-r reads.txt.gz \
-o subread results.bam