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The Subread package comprises a suite of software programs for processing next-gen sequencing read data.

Subread is available as a module on Apocrita.


To run the default installed version of Subread, simply load the subread module:

$ module load subread
$ subread-align

Version X.Y.Z


./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:

#$ -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