Minimap2¶
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.
Usage¶
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 ${NSLOTS} should be used.
Example job¶
Serial job¶
Here is an example job running on 1 core and 1GB of memory, using the test data from the Minimap2 GitHub repository, outputting in SAM format:
#!/bin/bash
#$ -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