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SkillsMP has collected 163 skills from PKU-EMBL/Metagenomics-Skills. Open a skill to review its source and details.
Showing 40 of 163 collected skills.
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.…
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…
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 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…
mlst — chromosomal multilocus sequence typing of assemblies against PubMLST schemes (Torsten Seemann wrapper). Use for isolate / HQ-MAG species ST calling. Upstream: https://github.com/tseemann/mlst. Route via cge-finders / microbial-mining for isolate…
PlasmidFinder — CGE in silico replicon / plasmid typing from assemblies or reads (BLAST/KMA vs PlasmidFinder DB). Use for Inc/replicon markers on isolates and HQ genomes. Upstream: https://github.com/genomicepidemiology/plasmidfinder. Route via cge-finders /…
pMLST — plasmid multilocus sequence typing from assemblies or reads using CGE / PubMLST plasmid schemes (IncI1, IncF, IncHI2, …). Use after PlasmidFinder replicon hits when a scheme ST is needed. Upstream: https://github.com/ssi-dk/pmlst (pmlst_ssi). Route…
ResFinder — CGE identification of acquired antimicrobial resistance genes (and optional PointFinder chromosomal mutations / DisinFinder biocide genes) from assemblies or reads. Use for isolate resistome typing with ResFinder DB phenotype mapping. Upstream:…
Choose shotgun tools by stage: QC, assembly, mapping, binning, taxonomic annotation, functional annotation, microbial mining, and research analysis (stats/figures). Use when deciding which skill to load — mappers, assemblers, ensemble binning (BASALT…
Identify plasmids, viruses, and other mobile genetic elements in assemblies or genomes. Use for plasmidome/virome mining, MGE-aware AMR context, and pre-CheckV viral candidate lists. Upstream: https://github.com/apcamargo/genomad.
MOB-suite — plasmid reconstruction and typing from draft assemblies (replicon, relaxase/MOB type, mate-pair, transferability, mash clusters). Use for plasmid compatibility / MOB typing and plasmid contig binning beyond geNomad scores. Upstream:…
MobileElementFinder — CGE detection of named mobile genetic elements (MITEs, IS, Tn, ComTn, ICE, IME, CIME, …) in assembled bacterial genomes, with optional ARG/virulence context. Use for isolate mobilome screens. Upstream: PyPI MobileElementFinder / CGE web…
PointFinder — CGE detection of antimicrobial resistance associated with chromosomal point mutations in selected bacterial pathogens. Use when acquired-gene screens miss mutation-driven resistance (e.g. gyrA, rpoB). DB: pointfinder_db; often run via ResFinder…
Antibiotic resistance gene annotation against CARD. Use this skill when working with rgi: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/arpcard/rgi. For routing across tools, use…
staramr — scan assemblies against ResFinder, PointFinder, and PlasmidFinder databases in one report (PHAC-NML). Use for isolate AMR + plasmid replicon summaries when you want CGE DBs without running each Finder separately. Upstream:…
VirulenceFinder — CGE virulence gene detection in bacterial assemblies/reads for supported species (historically E. coli, Enterococcus, S. aureus, Listeria, …). Upstream: https://bitbucket.org/genomicepidemiology/virulencefinder / PyPI Virulencefinder. Route…
Folddisco — fast discontinuous structural motif search across the protein universe (Steinegger lab). Use when: (1) Searching catalytic triads / zinc fingers / other short motifs in AFDB/PDB/ESM30, (2) Motif-level annotation after Foldseek fold hits, (3)…
Foldseek — ultrafast protein structure search and clustering via the 3Di structural alphabet (Steinegger / Söding labs). Use when: (1) Searching MAG or predicted structures against AFDB/PDB/ESM Atlas, (2) Foldseek-Multimer complex search for distant systems…
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…
Open MetaGenomic (OMG) corpus and gLM2 mixed-modality genomic language model — large pretraining data from IMG + MGnify (Tbp-scale DNA + billions of CDS). Use when: (1) Pretraining or evaluating genomic LMs, (2) Using gLM2 embeddings for function /…
Spacedust — de novo discovery of conserved gene clusters in microbial genomes using Foldseek structure comparison plus clustering/order-conservation statistics. Use when: (1) Finding conserved neighborhoods / modules in MAG collections, (2) Annotating dark…
Study design for shotgun metagenomics across QC, assembly, binning, and annotation. Use this skill when: (1) Deciding co-assembly vs sample-specific assembly, (2) Defining biological strata (time, treatment, habitat, host), (3) Building a…
ANCOM-BC / ANCOM-BC2 — compositionally aware differential abundance with sampling-fraction bias correction (Bioconductor ANCOMBC). Use when DA must account for compositionality and unequal sampling fractions; complements MaAsLin2/LEfSe. Upstream:…
MaAsLin2 / MaAsLin3 — multivariable association discovery between metadata and meta-omic features (taxonomy, pathways, genes) with filtering, normalization, transforms, and FDR control. Use for differential abundance with covariates or longitudinal designs.…
microeco — R package for modular microbiome downstream analysis and publication figures (diversity, composition, differential tests, networks, machine learning helpers). Use for end-to-end stats/plotting after MetaPhlAn/ Kraken/HUMAnN-style tables. Upstream:…
Nextflow — workflow manager for scalable, reproducible bioinformatics pipelines (DSL2, containers, cloud/HPC executors). Use when packaging shotgun metagenomics stages into portable runs or adopting nf-core modules/pipelines. Upstream:…
phyloseq — Bioconductor R package for storing and analyzing microbiome census data (OTU/ASV tables, taxonomy, phylogeny, sample data) with ggplot2 graphics. Use as a data container and classic analysis API; many DA/network tools accept phyloseq objects.…
Route downstream research analysis for shotgun metagenomics: QC reports (MultiQC), diversity/figures (visualization, microeco, phyloseq, STAMP), differential abundance (MaAsLin2/3, ANCOM-BC, LEfSe), association networks (SparCC, SPIEC-EASI), and workflow…
First-time environment and database setup for shotgun metagenomics tool skills. Use this skill when: (1) Installing Conda/Micromamba environments, (2) Preparing host, taxonomy, function, GTDB, or CheckM2 databases, (3) Installing BASALT weights, (4)…
Snakemake — Python-based workflow management for reproducible bioinformatics (rules, conda/container integration, cluster execution). Use when encoding shotgun metagenomics DAGs as Snakefiles or adopting community metagenomics snakemake pipelines. Upstream:…
SparCC — Sparse Correlations for Compositional data; infer taxon–taxon correlations from relative abundances without naive Pearson on compositions. Use for correlation networks on microbiome tables. Original: https://bitbucket.org/yonatanf/sparcc; convenient…
SPIEC-EASI — Sparse Inverse Covariance Estimation for Ecological Association Inference; compositionally robust microbial network inference (MB / glasso) with optional SparCC. Use for conditional association networks from count / relative abundance tables.…
STAMP — Statistical Analysis of Metagenomic Profiles; GUI for taxonomic / functional profile tests with effect sizes, CIs, and publication plots (extended error bars, PCA, heatmaps). Use for interactive exploratory DA and classic two-group/multi-group tests.…
LEfSe — Linear discriminant analysis Effect Size for metagenomic biomarker discovery between classes (taxa, genes, pathways). Use for classic LDA-style biomarkers and cladograms; prefer MaAsLin2/3 when many covariates or longitudinal designs are required.…
MultiQC — aggregate bioinformatics QC logs into a single interactive HTML report (FastQC, fastp, Bowtie2/BWA, Samtools, QUAST, …). Use after QC/mapping steps to audit libraries before biological statistics. Upstream: https://github.com/MultiQC/MultiQC. Route…
Statistical visualization checklist for shotgun metagenomics across QC, taxonomy, function, and binning outputs. Use when: (1) Choosing alpha/beta and composition figure types, (2) Labeling figures by stage and method, (3) Pairing plots with…
BioSurfDB — curated portal for biosurfactant production and hydrocarbon biodegradation genes/pathways with BLAST and related metagenome analysis helpers. Use for surfactant/biodegradation-focused searches and pathway browsing. Portal:…
Annotate carbohydrate-active enzymes (CAZymes) with dbCAN3 / run_dbcan on genomes or protein sets, including CGC finding and glycan substrate prediction (dbCAN-sub / dbCAN-PUL) relevant to dissolved organic matter (DOM) polymer processing. Use for CAZyme…
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),…
HADEG — curated Hydrocarbon Aerobic Degradation Enzymes and Genes database (alkanes, alkenes, aromatics, plastics) plus biosurfactant production genes with experimental evidence. Use to annotate MAG/contig proteins for HC biodegradation and biosurfactant…