| name | microbial-mining |
| description | Route microbial / genome mining after assembly or binning: BGCs (antiSMASH, BiG-SCAPE), AMR (RGI, DeepARG, ResFinder), mobile elements (geNomad, VirSorter2, CheckV, mobileOG-db, ISEScan, IntegronFinder, MOB-suite, CGE Finders), antimicrobial peptides (Macrel), element cycling (METABOLIC, MEBS, FeGenie), DOM/biosurfactant/HC biodegradation (dbCAN, HADEG, BioSurfDB), metabolism (DRAM, gapseq), defense (DefenseFinder, PADLOC), quorum sensing (QSAP), and annotation substrates (Bakta/Prokka). Use when the question is discovery of functional elements, not community tables alone.
|
| license | MIT |
| category | orchestration |
| tags | ["genome-mining","BGC","AMR","MGE","virus","metabolism","element-cycling","DOM","biosurfactant","defense","QS","routing"] |
| stage | mining |
Microbial mining
Mine assembled contigs and QC-filtered genomes/MAGs for functional elements.
Parallel track after assembly/binning — not a replacement for taxonomy tables.
Analytical thinking
| Claim type | Prefer | Caution |
|---|
| Natural products / BGCs | antismash → bigscape | Cluster ≠ characterized compound |
| AMR / resistome | rgi (± deeparg); isolates also resfinder / staramr | Hit ≠ expression / phenotype; keep CARD vs ResFinder separate |
| Plasmids / viruses (contig) | genomad, virsorter2, checkv, vcontact | CheckV before viral taxonomy |
| MGE protein machinery | mobileog | Category hit ≠ complete element |
| Insertion sequences | isescan | IS ≠ plasmid |
| Integrons / cassettes | integronfinder | Cassette ≠ expressed ARG |
| CGE Finders (+ pMLST / mlst / ABRicate) | cge-finders | Best on isolates / HQ MAGs |
| Plasmid MOB / replicon typing | mob-suite · plasmidfinder | Typing ≠ wet-lab Inc assay |
| Plasmid genome recovery | plasmaag | Multi-sample graphs help |
| Antimicrobial peptides | macrel | High candidate FDR |
| Element cycling (C/N/S/Fe/P/…) | element-cycling → metabolic / mebs / fegenie | Potential ≠ flux |
| DOM / glycans / biosurfactants / HC | dom-biosurfactant → dbcan / hadeg / biosurfdb | Hit ≠ assay / rate |
| Distilled metabolism | dram | Needs decent completeness |
| CAZymes (glycan DOM) | dbcan | Consensus + substrate rules |
| Genome-scale models |
Decision tree
Mining goal?
├─ BGCs → antismash → (many genomes) bigscape
├─ Resistome → rgi (± deeparg); isolates → resfinder / staramr (± pointfinder)
├─ Plasmids / viruses → genomad (± virsorter2) → checkv → vcontact
├─ MGE detail
│ ├─ Protein machinery → mobileog
│ ├─ IS elements → isescan
│ ├─ Integrons → integronfinder
│ ├─ CGE Finders → cge-finders (plasmidfinder · resfinder · abricate · …)
│ └─ Plasmid MOB/replicon typing → mob-suite / plasmidfinder (± pmlst)
├─ Plasmid MAGs → plasmaag (± genomad)
├─ Virulence markers (supported taxa) → virulencefinder / abricate
├─ Named MGEs (CGE library) → mobileelementfinder
├─ Chromosomal / plasmid ST → mlst / pmlst
├─ AMP smORFs → macrel
├─ Element cycling (C, N, S, Fe, P, H₂, CH₄, …) → element-cycling
├─ DOM / biosurfactant / HC biodegradation → dom-biosurfactant
├─ Metabolism distillate → dram (± dbcan)
├─ GEMs → gapseq
├─ Defense systems → bakta/prokka → defensefinder and/or padloc
├─ Quorum sensing → qsap
├─ Dark modules / neighborhoods → spacedust
├─ Structure / motif search → foldseek / folddisco
├─ Vector DB / warehouse search → homology-search
├─ LM remote homology → metagenomics-llm / protein-language-model
└─ Unsure → bakta on HQ MAGs, then branch
Typical order
bins/MAGs (checkm2 / mag-qc / gunc)
→ bakta | prokka
├─→ antismash → bigscape
├─→ rgi (± deeparg); isolates → cge-finders / staramr
├─→ element-cycling → metabolic / mebs / fegenie
├─→ dom-biosurfactant → dbcan / hadeg / biosurfdb
├─→ dram → dbcan / gapseq
├─→ defensefinder / padloc
└─→ qsap
contigs
→ genomad | virsorter2 → checkv → vcontact
→ mobileog / isescan / integronfinder / mob-suite
→ cge-finders (plasmidfinder · resfinder · virulencefinder · …)
→ plasmaag (multi-sample plasmid recovery)
→ macrel
Never
- Treat antiSMASH regions as proven natural products
- Publish viral genomes without CheckV
- Merge mining hits with HUMAnN abundances unlabeled
- Mine failed/low-quality bins without stating filters
- Claim elemental fluxes from HMM presence alone
Related skills
antismash · bigscape · genomad · virsorter2 · checkv · vcontact ·
mobileog · isescan · integronfinder · mob-suite · plasmaag ·
cge-finders · plasmidfinder · resfinder · pointfinder · disinfinder ·
virulencefinder · mobileelementfinder · pmlst · mlst · staramr ·
abricate · macrel ·
element-cycling · metabolic · mebs · fegenie · dom-biosurfactant ·
hadeg · biosurfdb · dram · dbcan · bakta · rgi · deeparg ·
gapseq · vmh · defensefinder · padloc · qsap · spacedust ·
foldseek · folddisco · homology-search · metagenomics-llm ·
tool-selection
