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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.


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:


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.

#$ -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}