metabinner

MetaBinner — stand-alone ensemble contig binning using multi-feature k-means components and two-stage single-copy-gene ensemble integration. Use when: (1) Running MetaBinner as an ensemble-style single tool, (2) Comparing to MetaWRAP/DAS Tool/COMEBin, (3) Diversifying bin sets before further refinement. Upstream: https://github.com/ziyewang/MetaBinner. For recommended multi-assembly refinement still prefer basalt ★.

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Repositório: PKU-EMBL/Metagenomics-Skills
Última atividade na origem: 3 de agosto de 2026 às 12:14
Idioma detectado do SKILL.md: inglês
Estrelas: 4
Forks: 0

Opções de instalação

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Instalar com Codex ou Claude Copie este prompt, cole no Codex, Claude ou outro assistente e deixe que ele revise a página da skill e instale para você.

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

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Prefere uma cópia local? Baixe os arquivos disponíveis atualmente no SkillsMP.

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SKILL.md

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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	metabinner
description	MetaBinner — stand-alone ensemble contig binning using multi-feature k-means components and two-stage single-copy-gene ensemble integration. Use when: (1) Running MetaBinner as an ensemble-style single tool, (2) Comparing to MetaWRAP/DAS Tool/COMEBin, (3) Diversifying bin sets before further refinement. Upstream: https://github.com/ziyewang/MetaBinner. For recommended multi-assembly refinement still prefer basalt ★.
license	MIT
category	analysis-tools
tags	["binning","MetaBinner","ensemble","SCG"]
upstream	https://github.com/ziyewang/MetaBinner
stage	binning

MetaBinner

Upstream: ziyewang/MetaBinner

Citation

Wang, Z. et al. MetaBinner: a high-performance and stand-alone ensemble binning method to recover individual genomes from complex microbial communities. Genome Biol. 24, 1 (2023). https://doi.org/10.1186/s13059-022-02832-6

Analytical thinking

MetaBinner is an internal ensemble: multiple k-means component binning results (multi-feature) integrated with SCG-aware two-stage selection — a stand-alone alternative to piping MetaBAT/MaxBin into MetaWRAP/DAS Tool.

Still feed outputs through CheckM2; for related multi-assembly catalogues prefer basalt ★. Complements comebin from the same group.

How to run

# follow upstream scripts — typically contigs + coverage tables
MetaBinner ...  # verify flags in README

Related skills

comebin · metawrap · dastool · basalt · checkm2 · tool-selection

metabinner

Informações da origem

Opções de instalação

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Mais deste repositório

Mais deste repositório

MetaBinner

Citation

Analytical thinking

How to run

Related skills

MetaBinner

Citation

Analytical thinking

How to run

Related skills