BWA is a fast light-weighted tool that aligns short sequences to a sequence database, such as the human reference genome. By default, BWA finds an alignment within edit distance 2 to the query sequence, except for disallowing gaps close to the end of the query. It can also be tuned to find a fraction of longer gaps at the cost of speed and of more false alignments.

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Slurm script

#!/bin/bash
#SBATCH --job-name=bwa
#SBATCH --time=1:00:00
#SBATCH --partition=norm
#SBATCH --ntasks=1
#SBATCH --mem=64GB
module load bwa
bwa index -a bwtsw file.csfasta
bwa aln -t $SLURM_CPUS_PER_TASK file.csfasta file.fastq > file.sai
bwa samse file.csfasta file.sai file.fastq > file.sam