Minimap2

Overview

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

Version 2.17 is installed on the CSF.

Restrictions on use

There are no restrictions on accessing this software on the CSF. It is release under the MIT License and all usage should adhere to that.

Set up procedure

We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for how to do this. Alternatively, you may load modulefiles on the login node and let the job inherit these settings.

Load one of the following modulefiles:

module load apps/binapps/minimap2/2.17
module load apps/binapps/minimap2/2.21

Running the application

Please do not run minimap2 on the login node. Jobs should be submitted to the compute nodes via batch.

Serial batch job submission

Create a batch submission script (which will load the modulefile in the jobscript), for example:

#!/bin/bash --login
#$ -cwd             # Job will run from the current directory
                    # NO -V line - we load modulefiles in the jobscript

# Load the version of the software you require
module load apps/binapps/minimap2/2.17

# $NSLOTS is automatically set to 1 for a serial (1-core) job
minimap2 -t $NSLOTS args...

Submit the jobscript using:

qsub scriptname

where scriptname is the name of your jobscript.

Parallel batch job submission