minimap

Official website : https://github.com/lh3/minimap2

1 Available version
2 Job submission script
- 2.1 index
- 2.2 align

Available version

Version	Module

Version	Module
2.26	minimap2/2.26-cpeGNU-23.03

Job submission script

index

#!/bin/bash
#SBATCH -p compute      # specific partition (compute,memory)
#SBATCH -N 1 -c 16      # -N 1 must be 1, -c can be 4, 8, 16, 32, 64 depending on the requirement
#SBATCH -t 24:00:00     # job time limit <hr:min:sec>
#SBATCH -A lt200xxx     # project ID
#SBATCH -J minimap-index    # job name

module restore
module load minimap2/2.26-cpeGNU-23.03

minimap2 -t $SLURM_CPUS_PER_TASK -d ref.mni ref.fasta

align

#!/bin/bash
#SBATCH -p compute     # specific partition (compute,memory)
#SBATCH -N 1 -c 128    # -N 1 must be 1, -c can be 4, 8, 16, 32, 64 depending on the requirement
#SBATCH -t 24:00:00    # job time limit <hr:min:sec>
#SBATCH -A lt200xxx    # project ID
#SBATCH -J minimap-align   # job name

module restore
module load minimap2/2.26-cpeGNU-23.03

minimap2 -t $SLURM_CPUS_PER_TASK -a ref.mni read.fastq > aligned.sam