gfatools is a set of tools for manipulating sequence graphs in the GFA or the rGFA format. It has implemented parsing, subgraph and conversion to FASTA/BED.

• gfatools Main Site

This application includes gfa-server, which can be used interactively via the HPC OnDemand web interface.

• Module Name: gfatools (see the modules page for more information)
• Environment variables set
  • GFATOOLS_HOME
• Example files in $GFATOOLS_HOME/test

Allocate an interactive session and run the program.
Sample session (user input in bold):

[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 gfatools

[user@cn3144 ~]$ gfatools view -l MTh4502 -r 1 $GFATOOLS_HOME/test/MT.gfa > sub.gfa

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

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

#!/bin/bash
set -e
module load gfatools
gfatools view -l MTh4502 -r 1 $GFATOOLS_HOME/test/MT.gfa > sub.gfa

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] gfatools.sh

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

gfatools stat sample1.gfa > sample1.txt
gfatools stat sample2.gfa > sample2.txt
gfatools stat sample3.gfa > sample3.txt
gfatools stat sample4.gfa > sample4.txt

Submit this job using the swarm command.

swarm -f gfatools.swarm [-g #] [-t #] --module gfatools