mebs

MEBS (Multigenomic Entropy-Based Score) — score genomes/metagenomes for biogeochemical cycle machinery via informative Pfam domains; strongest for sulfur (S), also supports N, O, CH4, and Fe cycle scores. Use for comparative cycle enrichment across large (meta)genome collections. Upstream: https://github.com/valdeanda/mebs (also eead-csic-compbio/metagenome_Pfam_score). Route via element-cycling. Gene-level Fe → fegenie; multi-element diagrams → metabolic.

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Repositorio: PKU-EMBL/Metagenomics-Skills
Última actividad en el origen: 3 de agosto de 2026 a las 13:47
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 mebs

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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	mebs
description	MEBS (Multigenomic Entropy-Based Score) — score genomes/metagenomes for biogeochemical cycle machinery via informative Pfam domains; strongest for sulfur (S), also supports N, O, CH4, and Fe cycle scores. Use for comparative cycle enrichment across large (meta)genome collections. Upstream: https://github.com/valdeanda/mebs (also eead-csic-compbio/metagenome_Pfam_score). Route via element-cycling. Gene-level Fe → fegenie; multi-element diagrams → metabolic.
license	MIT
category	analysis-tools
tags	["MEBS","sulfur","S","N","CH4","Fe","biogeochemistry","element-cycling"]
upstream	https://github.com/valdeanda/mebs
stage	mining

MEBS

Upstream: valdeanda/mebs · legacy/core: https://github.com/eead-csic-compbio/metagenome_Pfam_score

Citation

De Anda, V. et al. MEBS, a software platform to evaluate large (meta)genomic collections according to their metabolic machinery: unraveling the sulfur cycle. Gigascience 6, 1–17 (2017). https://doi.org/10.1093/gigascience/gix096

Analytical thinking

MEBS compresses curated cycle machinery into relative-entropy scores over Pfam domains. Benchmarked deeply on the sulfur (S) cycle; documentation also supports N, O, CH₄, and Fe scoring modes. Ideal for ranking many genomes/metagenomes by cycle “machinery presence,” not for drawing full METABOLIC-style pathway cartoons.

vs	Prefer MEBS when
`metabolic`	Comparative S/N/CH₄/Fe scores across large collections
`fegenie`	Score-level Fe vs explicit Fe gene neighborhoods
`dram`	Cycle enrichment metric vs distilled product tables

Input: directory of .faa peptide FASTA; use genomic vs metagenomic mode per docs (fragmentary metagenomes need the metagenomic entropy tables).

How to run

# clone / install per versioned README (v1.1 / v1.2 manuals differ)
# typical: mebs.pl -i pep_dir -t genomic|metagenomic …  (verify installed flags)

Decision tree

Cycle scoring need?
├─ S (or N/O/CH₄/Fe) entropy scores → mebs
├─ C/N/S diagrams + networks → metabolic
├─ Fe gene calls → fegenie
└─ Broad distillate → dram

Related skills

element-cycling · metabolic · fegenie · dram · microbial-mining · tool-selection

mebs

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Más de este repositorio

MEBS

Citation

Analytical thinking

How to run

Decision tree

Related skills

MEBS

Citation

Analytical thinking

How to run

Decision tree

Related skills