| name | antismash |
| description | Detect and annotate biosynthetic gene clusters (BGCs) on genomes and MAGs. Use for natural-product genome mining, choosing genefinding, interpreting region HTML/JSON, and stating validation limits. Upstream: https://github.com/antismash/antismash. Route via microbial-mining.
|
| license | MIT |
| category | analysis-tools |
| tags | ["BGC","secondary-metabolite","genome-mining"] |
| upstream | https://github.com/antismash/antismash |
| stage | mining |
antiSMASH
Upstream: antismash/antismash
Citation
Blin, K. et al. antiSMASH 7.0: new and improved predictions for detection,
regulation, chemical structures and visualisation. Nucleic Acids Res. 51,
W46–W50 (2023). https://doi.org/10.1093/nar/gkad344
Analytical thinking
antiSMASH finds BGC regions (PKS, NRPS, RiPP, terpene, …). It does not
prove a compound is produced. Fragmented MAGs truncate clusters — prefer
near-complete bins (checkm2 / mag-qc) and note contig breaks inside regions.
Run on per-genome FASTA (or GenBank from bakta/prokka), not mixed
community contigs, unless you explicitly want contig-level screens and will
not assign clusters to species without binning.
Record antiSMASH version and database download date. For comparative BGC
families across MAGs, follow with BiG-SCAPE (bigscape).
Prerequisites
| Requirement | Minimum | Recommended |
|---|
| Input | Genome/MAG FASTA | Completeness ≥50–70% for claims |
| DBs | download-antismash-databases | Shared read-only path |
| CPU | 8 | 16+ |
| Gene finding | prodigal (meta/MAGs) | Or use Bakta GenBank |
How to run
conda install -c bioconda antismash
download-antismash-databases
antismash bins/HQ_bin.fa \
--output-dir temp/antismash/${id} \
--html-title ${id} \
--cpus 16 \
--genefinding-tool prodigal \
--taxon bacteria
antismash temp/bakta/${id}/${id}.gbff \
--output-dir temp/antismash/${id} \
--cpus 16
Key parameters
| Option | Guidance |
|---|
--genefinding-tool prodigal | Default for MAG FASTA |
--taxon bacteria/fungi | Affects rules; match organism |
--cb-knownclusters / MiBIG opts | Enable when comparing to known BGCs (version-dependent) |
--minimal | Faster, fewer analyses — for screens only |
Outputs to archive
| Path | Meaning |
|---|
index.html | Interactive regions |
*.json / region GenBanks | Machine-readable clusters |
| stdout cluster counts | Summary for tables |
Decision tree
BGC mining goal?
├─ Single HQ MAG → bakta/prokka → antismash → (optional) bigscape
├─ Many MAGs catalogue → filter by checkm2 first, then batch antismash
└─ Need AMP smORFs not BGCs → macrel (different claim)
Troubleshooting
| Symptom | Action |
|---|
| DB missing errors | Re-run download-antismash-databases |
| Zero clusters on huge MAG | Check prodigal ran; try GenBank input |
| Huge runtime | Use --minimal for pilot; full mode for finals |
Related skills
microbial-mining · bakta · prokka · bigscape · dram · checkm2 · mag-qc
