Bowtie1 is a fast, multi-threaded, and memory efficient aligner for short read sequences. Bowtie uses a Burrows-Wheeler index to achieve a moderate memory footprint of 2 - 4 GB depending on genome size and alignment parameters. Performance generally scales well with thread count.

Documentation

Bowtie Manual

Slurm script

#!/bin/bash
#SBATCH --job-name=bowtie
#SBATCH --time=1:00:00
#SBATCH --partition=norm
#SBATCH --ntasks=1
#SBATCH --mem=64GB
module load bowtie
???