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 ${SLURM_NTASKS} 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
#SBATCH --ntasks=1 # (or -n 1) Request 1 core
#SBATCH --mem-per-cpu=1G # Request 1GB RAM per core (1GB total)
#SBATCH --time=1:0:0 # (or -t 1:0:0) Request 1 hour runtime
module load minimap2
# Produce mapping in SAM format
minimap2 -t ${SLURM_NTASKS} \
-a input.fa query.fa > output.sam