Gfatools

Introduction

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.

For more information, please check:

BioContainers: https://biocontainers.pro/tools/gfatools

Home page: https://github.com/lh3/gfatools

Versions

• 0.5

Commands

• gfatools

Module

You can load the modules by:

module load biocontainers
module load gfatools

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run gfatools on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=gfatools
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers gfatools

# Extract a subgraph
gfatools view -l MTh4502 -r 1 test/MT.gfa > sub.gfa

# Convert GFA to segment FASTA
gfatools gfa2fa test/MT.gfa > MT-seg.fa

# Convert rGFA to stable FASTA or BED
gfatools gfa2fa -s test/MT.gfa > MT.fa
gfatools gfa2bed -m test/MT.gfa > MT.bed