Variation graphs provide a succinct encoding of the sequences of many genomes. A variation graph (in particular as implemented in vg) is composed of:

• nodes, which are labeled by sequences and ids
• edges, which connect two nodes via either of their respective ends
• paths, which describe genomes, sequence alignments, and annotations (such as gene models and transcripts) as walks through nodes connected by edges

This model is similar to sequence graphs that have been used in assembly and multiple sequence alignment.

References:

• Garrison, E., Sirén, J., Novak, A. et al. Variation graph toolkit improves read mapping by representing genetic variation in the reference. Nature Biotechnology 36, 875–879 (2018)

• VG on GitHub
• Developers' Support Forum on Biostars

• Module Name: vg (see the modules page for more information)
• Some subcommands are multithreaded. See usage (e.g., vg giraffe --help).
• Environment variables set
  • VG_HOME
• Example files in $VG_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 vg

[user@cn3144 ~]$ vg construct -r $VG_HOME/test/small/x.fa -v $VG_HOME/test/small/x.vcf.gz > x.vg

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

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

#!/bin/bash
set -e
module load vg

vg autoindex --workflow giraffe -r $VG_HOME/test/small/x.fa -v $VG_HOME/test/small/x.vcf.gz -p x

vg sim -n 1000 -l 150 -x x.giraffe.gbz -a > x.sim.gam

vg giraffe -Z x.giraffe.gbz -G x.sim.gam -o BAM > aln.bam

Submit this job using the Slurm sbatch command.

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

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

vg giraffe -t $SLURM_CPUS_PER_TASK -Z x.giraffe.gbz -G x.sim.gam -o BAM > x-aln.bam
vg giraffe -t $SLURM_CPUS_PER_TASK -Z y.giraffe.gbz -G y.sim.gam -o BAM > y-aln.bam
vg giraffe -t $SLURM_CPUS_PER_TASK -Z z.giraffe.gbz -G z.sim.gam -o BAM > z-aln.bam

Submit this job using the swarm command.

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