BAM-format files are used to store alignment information and unaligned reads from next-generation sequencing machines. This tool is intended to extract raw sequences (with qualities) from a BAM file.

• https://gsl.hudsonalpha.org/information/software/bam2fastq

• Module Name: bam2fastq (see the modules page for more information)

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load bam2fastq
[user@cn3144 ~]$ bam2fastq input.bam -o outfile#
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. bam2fastq.sh). For example:

#!/bin/bash
set -e
module load bam2fastq
bam2fastq input.bam -o outfile#

Submit this job using the Slurm sbatch command.

sbatch bam2fastq.sh

Create a swarmfile (e.g. bam2fastq.swarm). For example:

cd dir1; bam2fastq input.bam -o outfile#
cd dir2; bam2fastq input.bam -o outfile#
cd dir3; bam2fastq input.bam -o outfile#

Submit this job using the swarm command.

swarm -f bam2fastq.swarm [-t #] --module bam2fastq