Pangene is a command-line tool to construct a pangenome gene graph. In this graph, a node repsents a marker gene and an edge between two genes indicates their genomic adjaceny on input genomes. Pangene takes the miniprot alignment between a protein set and multiple genomes and produces a graph in the GFA format. It attempts to reduce the redundancy in the input proteins and filter spurious alignments while preserving close but non-identical paralogs. The output graph can be visualized in generic GFA viewers such as BandageNG or via the GFA Server app on Biowulf OnDemand.

References:

• H Li, M Marin, MR Farhat. (2024) Exploring gene content with pangene graphs. arXiv:2402.16185

• Pangene Main Site
• Prebuilt pangene graphs

• Module Name: pangene (see the modules page for more information)
• Environment variables set
  • PANGENE_HOME
• Example files in $PANGENE_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 pangene
[user@cn3144 ~]$ man pangene # Read the manual (Press q to exit it once finished)
[user@cn3144 ~]$ pangene $PANGENE_HOME/test/C4/*.paf.gz > C4.gfa
[user@cn3144 ~]$ pangene.js call C4.gfa > C4.bubble.txt
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

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

#!/bin/bash
set -e
module load pangene
pangene $PANGENE_HOME/test/C4/*.paf.gz > C4.gfa
pangene.js call C4.gfa > C4.bubble.txt

Submit this job using the Slurm sbatch command.

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

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

pangene *.sample1.paf > sample1.gfa
pangene *.sample2.paf > sample2.gfa
pangene *.sample3.paf > sample3.gfa
pangene *.sample4.paf > sample4.gfa

Submit this job using the swarm command.

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