Biowulf High Performance Computing at the NIH
ngsutils on Biowulf

NGSUtils is a suite of software tools for working with next-generation sequencing datasets. NGSUtils is made up of 50+ programs, mainly written in Python. These are separated into modules based on the type of file that is to be analyzed. There are four modules:

ngsutilsj is a java-based version of ngsutils

Each of these modules contains many commands for manipulating, filtering, converting, or analyzing these types of files.

NGSutils was developed at Indiana U. & Stanford School of Medicine.

Documentation
Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

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 ~]$ bamutils expressed HCT-116.bam
   0.0% - 0:00 [>                   ] ETA:  | chr1:726991chr1	9974	10083	region_1	2	+
chr1	12828	13139	region_4	17	+
chr1	12992	13365	region_5	18	-
chr1	13200	13539	region_6	66	+
[...]

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Batch job
Most jobs should be run as batch jobs.

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

#!/bin/bash
set -e
module load ngsutils
cd /data/$USER/somedir
bamutils expressed HCT-116.bam

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] ngsutils.sh
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

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

fastqutils    revcomp    file1.fas
fastqutils    revcomp    file2.fas
fastqutils    revcomp    file3.fas
[...]

Submit this job using the swarm command.

swarm -f ngsutils.swarm [-g #] --module ngsutils
where
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
--module ngsutils Loads the ngsutils module for each subjob in the swarm