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NGS QC Toolkit on Biowulf & Helix

NGS QC Toolkit: A toolkit for the quality control (QC) of next generation sequencing (NGS) data. The toolkit comprises of user-friendly stand alone tools for quality control of the sequence data generated using Illumina and Roche 454 platforms with detailed results in the form of tables and graphs, and filtering of high-quality sequence data. It also includes few other tools, which are helpful in NGS data quality control and analysis.

Running on Helix

$ module load ngsqctoolkit
$ cd /data/$USER/dir
$ IlluQC.pl <options>

Running a single batch job on Biowulf

1. Create a script file. The file will contain the lines similar to the lines below.

#!/bin/bash


module load ngsqctoolkit
cd /data/$USER/dir
IlluQC.pl <options>

2. Submit the script on biowulf:

$ sbatch jobscript

If more momory is required (default 4gb), specify --mem=Mg, for example --mem=10g:

$ sbatch --mem=10g jobscript

Running a swarm of jobs on Biowulf

Setup a swarm command file:

  cd /data/$USER/dir1; IlluQC.pl <options>
  cd /data/$USER/dir2; IlluQC.pl <options>
  cd /data/$USER/dir2; IlluQC.pl <options>
	[......]
  

Submit the swarm file, -f specify the swarmfile name, and --module will be loaded the required module for each command line in the file:

  $ swarm -f swarmfile --module ngsqctoolkit

If more memory is needed for each line of commands, the below example allocate 10g for each command:

  $ swarm -f swarmfile -g 10 --module ngsqctoolkit

For more information regarding running swarm, see swarm.html

Running an interactive job on Biowulf

It may be useful for debugging purposes to run jobs interactively. Such jobs should not be run on the Biowulf login node. Instead allocate an interactive node as described below, and run the interactive job there.

biowulf$ sinteractive 
salloc.exe: Granted job allocation 16535

cn999$ module load ngsqctoolkit
cn999$ cd /data/$USER/dir
cn999$ IlluQC.pl <options>
[...etc...]

cn999$ exit
exit

biowulf$

Make sure to exit the job once finished.

If more memory is needed, use --mem. For example

biowulf$ sinteractive --mem=8g

Documentation

http://www.nipgr.res.in/ngsqctoolkit.html