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Meerkat is designed to identify structural variations from paired end high throughput sequencing data. It predicts structural variations from discordant read pairs then it looks for reads that cover the predicted breakpoints junctions, refines breakpoints by local alignments and predicts mechanisms that structural variations are formed.

Meerkat is available as a module on Apocrita.


To run the default installed version of Meerkat, simply load the meerkat module:

module load meerkat

For usage documentation, run -h.

Example job

Serial job

Here is an example job running on 1 core and 2GB of memory:

#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=2G

module load meerkat -b example.bam \
               -I example.fasta \
               -A example.fasta.fai -b example.bam \
           -F /path/to/reference/fasta/files -b example.bam \
             -R /path/to/repeat_mask_file