Isaac Aligner¶
Isaac Aligner is designed to align next-generation sequencing data with low-error rates (single or paired-ends).
Isaac Aligner is available as a module on Apocrita.
Usage¶
To run the default installed version of Isaac Aligner, simply load the
isaac-aligner module:
$ module load isaac-aligner
Usage: <command> [options] [--help]
The following commands are available:
isaac-align
isaac-merge-references
isaac-pack-reference
isaac-reorder-reference
Usage for each command can be shown by running the command with the --help
option. For more detailed documentation, please check the link to the
documentation page listed in the references below.
Example job¶
Analyse a pair of fastq files and produce bam output.
It is important that the value used for h_vmem matches the value given
for the -m option. Mismatches could result in job termination due to
insufficient memory.
Please be sure to add the argument -j ${NSLOTS} to your run command. This
will ensure the number of compute threads isaac-aligner spawns matches the
number of cores requested in your job script. See
here for more information.
#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=20G
module load isaac-aligner
isaac-align -r /path/to/sorted-reference.xml \
-b <Run_Folder>/Data/Intensities/BaseCalls \
-m 20 \
-j ${NSLOTS}