| name | gunc |
| description | Detect chimerism/contamination in prokaryotic genomes/MAGs. Use this skill when working with gunc: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/grp-bork/gunc. For stage routing use tool-selection / metagenomics-workflow.
|
| license | MIT |
| category | analysis-tools |
| tags | ["qc","contamination","chimerism"] |
| upstream | https://github.com/grp-bork/gunc |
| stage | assessment |
GUNC
Upstream: GUNC
Citation
Orakov, A. et al. GUNC: detection of chimerism and contamination in prokaryotic genomes. Genome Biol. 22, 178 (2021). https://doi.org/10.1186/s13059-021-02393-0
See also docs/references.md.
Analytical thinking
CheckM-style metrics estimate surplus marker copies but under-detect some
clade-level chimeras (contigs from distinct lineages merged into one bin).
GUNC was built for those underdetected contamination types; the paper
conservatively estimated substantial residual contamination in public genomes
even after conventional QC.
Use GUNC with CheckM2 before strong claims on novel lineages, GEMs, or
BGCs tied to a single MAG. Contamination types to keep distinct in text:
| Type | Rough meaning |
|---|
| Redundant | Extra copies from related genome content |
| Non-redundant / chimeric | Foreign-lineage fragments in one “genome” |
Single-coverage binning can hide co-abundant contaminants within one sample —
multi-coverage binning + GUNC is a strong pair (Mattock & Watson 2023).
How to run
conda install -c bioconda gunc
gunc run -i bins/ --db_file $GUNC_DB -r temp/gunc -t 16
Key parameters
| Item | Notes |
|---|
| DB | Download/pin GUNC DB |
| With CheckM2 | Combine filters; discordant calls → manual review |
| Novel lineages | Higher scrutiny; GUNC DB taxonomy limits apply |
Related skills
checkm2 · mag-qc · drep · basalt · study-design · tool-selection
