The Pangenome Graph Builder (pggb) builds pangenome variation graphs from a set of input sequences.

A pangenome variation graph is a kind of generic multiple sequence alignment. It lets us understand any kind of sequence variation between a collection of genomes. It shows us similarity where genomes walk through the same parts of the graph, and differences where they do not.

pggb generates this kind of graph using an all-to-all alignment of input sequences (wfmash), graph induction (seqwish), and progressive normalization (smoothxg, gfaffix). After construction, pggb generates diagnostic visualizations of the graph (odgi). A variant call report (in VCF) representing both small and large variants can be generated based on any reference genome included in the graph (vg). pggb writes its output in GFAv1 format, which can be used as input by numerous "genome graph" and pangenome tools, such as the vg and odgi toolkits.

pggb has been tested at scale in the Human Pangenome Reference Consortium (HPRC) as a method to build a graph from the draft human pangenome.

References:

• Erik Garrison*, Andrea Guarracino*, Simon Heumos, Flavia Villani, Zhigui Bao, Lorenzo Tattini, Jörg Hagmann, Sebastian Vorbrugg, Santiago Marco-Sola, Christian Kubica, David G. Ashbrook, Kaisa Thorell, Rachel L. Rusholme-Pilcher, Gianni Liti, Emilio Rudbeck, Sven Nahnsen, Zuyu Yang, Mwaniki N. Moses, Franklin L. Nobrega, Yi Wu, Hao Chen, Joep de Ligt, Peter H. Sudmant, Nicole Soranzo, Vincenza Colonna, Robert W. Williams, Pjotr Prins. Building pangenome graphs. Nature Methods (2024)

• pggb main site
• pggb on GitHub

• Module Name: pggb (see the modules page for more information)
• Multithreaded using the -t/--threads and --poa-threads flags.
• Use local scratch for temporary files with the -D/--temp-dir flag (see example below).
• Environment variables set
  • PGGB_HOME
• Example files in $PGGB_HOME/data

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

[user@biowulf]$ sinteractive --gres lscratch:10 --cpus-per-task 6 --mem 16g
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 pggb

[user@cn3144 ~]$ pggb -i $PGGB_HOME/data/HLA/DRB1-3123.fa.gz -n 12 -t $SLURM_CPUS_PER_TASK -o out -M --temp-dir /lscratch/$SLURM_JOB_ID

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

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

#!/bin/bash
set -e
module load pggb
pggb -i $PGGB_HOME/data/HLA/DRB1-3123.fa.gz -n 12 -t $SLURM_CPUS_PER_TASK -V 'gi|568815561' -o out -M --temp-dir /lscratch/$SLURM_JOB_ID

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=# [--mem=#] --gres lscratch:# pggb.sh

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

pggb -i output/DRB1-3123.fa.gz.bf3285f.community.0.fa \
     -o output/DRB1-3123.fa.gz.bf3285f.community.0.fa.out \
     -s 5000 -l 25000 -p 90 -c 1 -K 19 -F 0.001 -g 30 \
     -k 23 -f 0 -B 10M \
     -n 12 -j 0 -e 0 -G 700,900,1100 -p 1,4,6,2,26,1 -O 0.001 -d 100 -Q Consensus_ \
     -Y "#" --temp-dir /lscratch/$SLURM_JOB_ID --threads $SLURM_CPUS_PER_TASK --poa-threads $SLURM_CPUS_PER_TASK
pggb -i output/DRB1-3123.fa.gz.bf3285f.community.1.fa \
     -o output/DRB1-3123.fa.gz.bf3285f.community.1.fa.out \
     -s 5000 -l 25000 -p 90 -c 1 -K 19 -F 0.001 -g 30 \
     -k 23 -f 0 -B 10M \
     -n 12 -j 0 -e 0 -G 700,900,1100 -p 1,4,6,2,26,1 -O 0.001 -d 100 -Q Consensus_ \
     -Y "#" --temp-dir /lscratch/$SLURM_JOB_ID --threads $SLURM_CPUS_PER_TASK --poa-threads $SLURM_CPUS_PER_TASK

You can use the partition-before-pggb command to help create the swarmfile for you by preparing the input and generating the commands.

Submit this job using the swarm command.

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