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Minimap2 is a versatile sequence alignment program that aligns DNA or Messenger RNA sequences against a large reference database.

Minimap2 is available as a module on Apocrita.


To run the default installed version of Minimap2, simply load the minimap2 module:

$ module load minimap2
$ minimap2 --help

Usage: minimap2 [options] <target.fa>|<target.idx> [query.fa] [...]

For full usage documentation, run minimap2 --help.

Core Usage

To ensure that Minimap2 always uses the correct number of cores, the number of threads option -t ${NSLOTS} should be used.

Example job

Serial job

Here is an example job running on 1 core and 1GB of memory, using the test data from the Minimap2 GitHub repository, outputting in SAM format:

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

module load minimap2

# Produce mapping in SAM format
minimap2 -t ${NSLOTS} \
         -a input.fa query.fa > output.sam