metagenomics-workflow

End-to-end shotgun metagenomics: quality control, assembly, mapping, binning, taxonomic annotation, functional annotation, microbial mining (BGCs, AMR, MGEs, element cycling, DOM, defense), and research analysis (stats/figures). Use when starting a project or ordering stages. For tool choice use tool-selection. For mining use microbial-mining; for paper stats use research-analysis. For public DBs use public-databases.

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Repositorio: PKU-EMBL/Metagenomics-Skills
Última actividad en el origen: 3 de agosto de 2026 a las 14:28
Idioma detectado de SKILL.md: inglés
Estrellas: 4
Forks: 0

Opciones de instalación

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npx skills add https://github.com/PKU-EMBL/Metagenomics-Skills --skill metagenomics-workflow

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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	metagenomics-workflow
description	End-to-end shotgun metagenomics: quality control, assembly, mapping, binning, taxonomic annotation, functional annotation, microbial mining (BGCs, AMR, MGEs, element cycling, DOM, defense), and research analysis (stats/figures). Use when starting a project or ordering stages. For tool choice use tool-selection. For mining use microbial-mining; for paper stats use research-analysis. For public DBs use public-databases.
license	MIT
category	orchestration
tags	["guidance","pipeline","workflow","QC","assembly","mapping","binning","taxonomy","function","mining","research-analysis"]

Goal	Route
Composition only	QC → `metaphlan` / `singlem` / `kraken2` → `research-analysis`
Genome-resolved catalogue	QC → assembly → mapping → `basalt` ★ → mag-qc → gtdbtk
Interactive MAG polish	After auto-bins → `anvio` → re-QC
Environmental unknowns	QC → `singlem` (± `binchicken` coassembly)
Viral ecology	contigs → `genomad`/`virsorter2` → `checkv` → `vcontact`

name	metagenomics-workflow
description	End-to-end shotgun metagenomics: quality control, assembly, mapping, binning, taxonomic annotation, functional annotation, microbial mining (BGCs, AMR, MGEs, element cycling, DOM, defense), and research analysis (stats/figures). Use when starting a project or ordering stages. For tool choice use tool-selection. For mining use microbial-mining; for paper stats use research-analysis. For public DBs use public-databases.
license	MIT
category	orchestration
tags	["guidance","pipeline","workflow","QC","assembly","mapping","binning","taxonomy","function","mining","research-analysis"]

Goal	Route
Composition only	QC → `metaphlan` / `singlem` / `kraken2` → `research-analysis`
Genome-resolved catalogue	QC → assembly → mapping → `basalt` ★ → mag-qc → gtdbtk
Interactive MAG polish	After auto-bins → `anvio` → re-QC
Environmental unknowns	QC → `singlem` (± `binchicken` coassembly)
Viral ecology	contigs → `genomad`/`virsorter2` → `checkv` → `vcontact`

metagenomics-workflow

Opciones de instalación

Revisa los archivos de origen