Genome UNClutterer (GUNC) is a tool for detection of chimerism and contamination in prokaryotic genomes resulting from mis-binning of genomic contigs from unrelated lineages. It does so by applying an entropy based score on taxonomic assignment and contig location of all genes in a genome.

References:

• Orakov, A., Fullam, A., Coelho, L.P. et al. GUNC: Detection of Chimerism and Contamination in Prokaryotic Genomes Genome Biol 22, 178 (2021)

• Gunc Main Site

• Module Name: gunc (see the modules page for more information)

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 gunc
[+] Loading gunc  1.0.5 on cn3144
[+] Loading singularity  4.1.5 on cn3144

[user@cn3144 ~]$  gunc -h 
usage: gunc [-h] [-v]  ...

Tool for detection of chimerism and contamination in prokaryotic genomes.

options:
  -h, --help     show this help message and exit
  -v, --version  Print version number and exit.

GUNC subcommands:

    run          Run chimerism detection.
    download_db  Download GUNC db.
    merge_checkm
                 Merge GUNC and CheckM outputs.
    plot         Create interactive visualisation.
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

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

#!/bin/bash
set -e
module load TEMPLATE
TEMPLATE < TEMPLATE.in > TEMPLATE.out

Submit this job using the Slurm sbatch command.

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

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

TEMPLATE < TEMPLATE.in > TEMPLATE.out
TEMPLATE < TEMPLATE.in > TEMPLATE.out
TEMPLATE < TEMPLATE.in > TEMPLATE.out
TEMPLATE < TEMPLATE.in > TEMPLATE.out

Submit this job using the swarm command.

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