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SkillsMP has collected 163 skills from PKU-EMBL/Metagenomics-Skills. Open a skill to review its source and details.
PKU-EMBL/Metagenomics-SkillsShowing 40 of 163 collected skills.
Use EMBL-EBI MGnify for analysed microbiome studies and biome genome catalogues (including UHGG / human-gut and other biomes). Use this skill when: (1) Browsing or citing MGnify analyses, (2) Downloading UHGG or other MGnify Genomes catalogues, (3) Searching…
proGenomes4 — nearly 2 million consistently QC'd and annotated high-quality prokaryotic genomes with habitat metadata, pan-genomes, MGE/BGC annotations. Use when: (1) Building large microbial genome reference sets, (2) Comparative genomics / pan-genome…
PKU-EMBL BASALT and BASALT-Air — recommended ensemble MAG recovery across one or more assemblies (multi-binner + refinement). Use this skill when: (1) Running BASALT multi-binner recovery, (2) Choosing Conda BASALT vs BASALT-Air, (3) Multi-assembly…
Bayesian re-estimation of abundance from Kraken2 reports. Use this skill when working with bracken: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/jenniferlu717/Bracken. For stage…
ML-based MAG completeness and contamination estimation. Use this skill when working with checkm2: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/chklovski/CheckM2. For routing across…
COMEBin — contrastive multi-view representation learning for metagenomic contig binning (composition + coverage). Use when: (1) Running COMEBin as a modern single binner, (2) Comparing to SemiBin2/VAMB/MetaBAT2, (3) Co- assembly, single-sample, or…
Calculate coverage/relative abundance of genomes or contigs. Use this skill when working with coverm: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/wwood/CoverM. For routing across…
DAS Tool (Dereplication, Aggregation and Scoring) integrates multiple binning predictions into one non-redundant MAG set for a single assembly. Use this skill when working with DAS_Tool: preparing contig2bin tables, choosing score thresholds, comparing…
Ultra-fast protein alignment (BLASTP/X alternative) for functional/taxonomic searches. Use this skill when working with diamond: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream:…
Detect chimerism/contamination in prokaryotic genomes/MAGs. Use this skill when working with gunc: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/grp-bork/gunc. For stage routing use…
Strain-level microdiversity and shared-strain detection from metagenomes. Use this skill when working with instrain: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/MrOlm/inStrain. For…
k-mer taxonomic classification; pair with Bracken for abundance. Use this skill when working with kraken2: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/DerrickWood/kraken2. For…
LorBin — unsupervised long-read metagenome binning with multiscale adaptive clustering (DBSCAN + BIRCH) and single-copy-gene evaluation. Use when: (1) Binning long-read / HiFi metagenome assemblies, (2) Recovering MAGs from species-rich or…
Metabuli — metagenomic taxonomic classification via joint DNA + amino-acid (metamer) analysis for sensitive homology and specific close-taxon resolution. Use when: (1) Choosing a classifier beyond DNA-only (Kraken2) or AA-only (Kaiju), (2) Profiling…
Marker-gene taxonomic profiling of metagenomes. Use this skill when working with metaphlan: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/biobakery/MetaPhlAn. For routing across…
MetaWRAP suite for multi-binner MAG recovery and CheckM-style bin refinement — one option in the ensemble binning family (with DAS Tool and BASALT). Use this skill when working with metawrap: installing, choosing parameters, running…
Marker-gene taxonomic profiling across environments (mOTUs3). Use this skill when working with motus: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/motu-tool/mOTUs. For stage routing…
Self-supervised contrastive learning binning for short- and long-read assemblies. Use this skill when working with semibin2: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream:…
Rapid species-level metagenome profiling and containment estimation. Use this skill when working with sylph: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/bluenote-1577/sylph. For…
Deep variational autoencoder binning of metagenome contigs. Use this skill when working with vamb: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/RasmussenLab/vamb. For stage routing…
Detect and annotate biosynthetic gene clusters (BGCs) on genomes and MAGs. Use for natural-product genome mining, choosing genefinding, interpreting region HTML/JSON, and stating validation limits. Upstream: https://github.com/antismash/antismash. Route via…
Cluster and compare biosynthetic gene clusters across genomes with BiG-SCAPE (similarity networks of antiSMASH regions). Use after batch antiSMASH for BGC family discovery. Upstream: https://github.com/medema-group/BiG-SCAPE.
Gapped short-read alignment to contigs/genomes for coverage used in binning and abundance. Use when indexing assemblies, mapping cleaned PE reads, choosing sensitivity presets, QC of BAM rates, or preparing depths for MetaBAT2/CoverM/BASALT. Upstream:…
Architecture-aware faster BWA-MEM for Illumina reads to contigs/genomes. Use when a BWA-MEM workflow is required but throughput must improve, or when migrating from classic bwa mem. Upstream: https://github.com/bwa-mem2/bwa-mem2. Index format is NOT…
Distill microbial metabolism annotations for MAGs/genomes into curated product tables (DRAM annotate + distill). Use for ecological functional potential, pathway summaries, and MAG metabolism figures. Upstream: https://github.com/WrightonLabCSU/DRAM.
Adaptive contig binning from tetranucleotide composition and multi-sample coverage. Use for primary single-binner runs feeding DAS Tool, MetaWRAP, or BASALT ensembles. Upstream: https://bitbucket.org/berkeleylab/metabat.
Polish genome assemblies and fix small errors using short-read BAM evidence. Use after mapping Illumina reads to a draft assembly (including long-read drafts). Upstream: https://github.com/broadinstitute/pilon.
Ultrafast consensus polishing of assemblies using mapped long (or short) reads. Use after long-read or hybrid assembly before binning/annotation. Upstream: https://github.com/lbcb-sci/racon.
SAM/BAM/CRAM processing for metagenomic mapping outputs — sort, index, flagstat, coverage, and filtering. Use whenever an aligner writes SAM/BAM before CoverM, MetaBAT2, inStrain, or BASALT. Upstream: https://github.com/samtools/samtools.
Ultra-fast short-read alignment with flexible seed size for metagenome coverage mapping. Use when mapping many Illumina samples to large contig sets before binning, or when Bowtie2/BWA is the throughput bottleneck. Upstream:…
Install and pin bioBakery reference databases for MetaPhlAn and HUMAnN (ChocoPhlAn markers, UniRef gene families, MetaCyc pathways, utility mapping). Use this skill when: (1) Downloading MetaPhlAn/HUMAnN databases, (2) Choosing UniRef90 vs UniRef50, (3)…
Cluster genes/proteins to build non-redundant catalogues. Use this skill when working with cd-hit: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/weizhongli/cdhit. For routing across…
Deep-learning prediction of antibiotic resistance genes from metagenomic data. Use this skill when working with deeparg: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream:…
Dereplicate microbial genomes by ANI to species/strain catalogues. Use this skill when working with drep: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/MrOlm/drep. For routing across…
Ultra-fast FASTQ QC/adapter trimming for Illumina/MGI short reads. Use this skill when working with fastp: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/OpenGene/fastp. For routing…
Gene-family and pathway abundance profiling from metagenomes. Use this skill when working with humann: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/biobakery/humann. For routing…
QC wrapper focused on host (and contaminant) read removal via Bowtie2. Use this skill when working with kneaddata: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/biobakery/kneaddata.…
Screen genomes and metagenomes for antimicrobial peptides (AMPs). Use this skill when working with macrel: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/BigDataBiology/macrel. For…
Ultra-fast memory-efficient metagenome assembler. Use this skill when working with megahit: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/voutcn/megahit. For routing across tools, use…
More sensitive metagenomic assembly via SPAdes meta mode. Use this skill when working with metaspades: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/ablab/spades. For routing across…