dom-biosurfactant

Route dissolved organic matter (DOM) / glycan substrate capacity, biosurfactant production, and hydrocarbon/plastic biodegradation annotation for shotgun metagenomics. Covers “like-dissolves-like” solubility-related microbial functions: CAZyme–glycan (dbCAN), biosurfactants + HC degradation (HADEG, BioSurfDB), and related BGC context (antiSMASH). Child skills: hadeg, biosurfdb; also dbcan, antismash, dram. Route via microbial-mining.

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Repository: PKU-EMBL/Metagenomics-Skills
Last source activity: August 3, 2026 at 14:06
Detected SKILL.md language: English
Stars: 4
Forks: 0

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abricate

ABRicate — mass screening of contigs for AMR/virulence/plasmid markers against bundled databases (ResFinder, CARD, NCBI, VFDB, PlasmidFinder, EcoLI_VF, ARG-ANNOT, MEGARES, …). Use for fast multi-DB isolate or MAG screens and database concordance checks. Upstream: https://github.com/tseemann/abricate. Route via cge-finders / microbial-mining; official CGE CLI still via resfinder/plasmidfinder when phenotype mapping or PointFinder is required.

2026-08-03

cge-finders

Route Center for Genomic Epidemiology (CGE) Finder-style screens and related isolate typing: PlasmidFinder, ResFinder, PointFinder, DisinFinder, VirulenceFinder, MobileElementFinder, pMLST, plus staramr / ABRicate wrappers and chromosomal mlst. Use for clinical/One-Health isolate typing and plasmid-borne AMR context — not community-wide dark-matter discovery. Child skills: plasmidfinder, resfinder, pointfinder, disinfinder, virulencefinder, mobileelementfinder, pmlst, staramr, abricate, mlst. Complements genomad, mob-suite, rgi, mobileog. Route via microbial-mining.

2026-08-03

disinfinder

DisinFinder — CGE disinfectant / biocide resistance gene screen via the DisinFinder database, typically run through ResFinder. Use for isolate biocide-resistance markers alongside acquired AMR. DB: https://bitbucket.org/genomicepidemiology/disinfinder_db. Route via cge-finders / resfinder / microbial-mining.

2026-08-03

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name	dom-biosurfactant
description	Route dissolved organic matter (DOM) / glycan substrate capacity, biosurfactant production, and hydrocarbon/plastic biodegradation annotation for shotgun metagenomics. Covers “like-dissolves-like” solubility-related microbial functions: CAZyme–glycan (dbCAN), biosurfactants + HC degradation (HADEG, BioSurfDB), and related BGC context (antiSMASH). Child skills: hadeg, biosurfdb; also dbcan, antismash, dram. Route via microbial-mining.
license	MIT
category	orchestration
tags	["DOM","biosurfactant","hydrocarbon","biodegradation","CAZyme","solubility","HADEG"]
stage	mining