pku-embl

AAMB / AVAMB — adversarial autoencoder metagenomic binning and its ensemble with VAMB for improved near-complete MAG recovery. Use...

ABRicate — mass screening of contigs for AMR/virulence/plasmid markers against bundled databases (ResFinder, CARD, NCBI, VFDB, Pla...

AlphaGEM — genome-scale metabolic modelling aided by protein structure alignment and deep-learning dark-metabolism mining. Use whe...

ANCOM-BC / ANCOM-BC2 — compositionally aware differential abundance with sampling-fraction bias correction (Bioconductor ANCOMBC)....

Detect and annotate biosynthetic gene clusters (BGCs) on genomes and MAGs. Use for natural-product genome mining, choosing genefin...

Anvi'o — interactive multi-omics platform for metagenomic assemblies, MAG refinement, visualization, and SNP/profile exploration. ...

Rapid standardized annotation of bacterial genomes (alignment-free ID). Use for installation, parameter choice, execution, output ...

Basic rapid ribosomal RNA predictor for genomes. Use for installation, parameter choice, execution, output interpretation, or trou...

PKU-EMBL BASALT and BASALT-Air — recommended ensemble MAG recovery across one or more assemblies (multi-binner + refinement). Use ...

Fast splice-aware aligner and BBTools suite utilities (BBMerge, etc.). Use for installation, parameter choice, execution, output i...

Cluster and compare biosynthetic gene clusters across genomes with BiG-SCAPE (similarity networks of antiSMASH regions). Use after...

Bin Chicken — targeted coassembly planning for recovering low-abundance / novel MAGs by grouping metagenomes that share marker-gen...

Install and pin bioBakery reference databases for MetaPhlAn and HUMAnN (ChocoPhlAn markers, UniRef gene families, MetaCyc pathways...

BioSurfDB — curated portal for biosurfactant production and hydrocarbon biodegradation genes/pathways with BLAST and related metag...

Gapped short-read alignment to contigs/genomes for coverage used in binning and abundance. Use when indexing assemblies, mapping c...

Bayesian re-estimation of abundance from Kraken2 reports. Use for installation, parameter choice, execution, output interpretation...

Benchmarking Universal Single-Copy Orthologs for genome completeness. Use for installation, parameter choice, execution, output in...

Burrows–Wheeler short-read alignment (BWA-MEM) to contigs/genomes. Use for installation, parameter choice, execution, output inter...

pku-embl/metagenomics-skills

Caduceus — bi-directional equivariant long-range DNA language model (Mamba / RC-aware) for long genomic contexts. Use when: (1) Lo...

pku-embl/metagenomics-skills

Cluster genes/proteins to build non-redundant catalogues. Use for installation, parameter choice, execution, output interpretation...

pku-embl/metagenomics-skills

ML-based MAG completeness and contamination estimation. Use for installation, parameter choice, execution, output interpretation, ...

Quality assessment of metagenome-assembled viral genomes. Use for installation, parameter choice, execution, output interpretation...

COMEBin — contrastive multi-view representation learning for metagenomic contig binning (composition + coverage). Use when: (1) Ru...

Composition and coverage binning of metagenomic contigs. Use for installation, parameter choice, execution, output interpretation,...

Calculate coverage/relative abundance of genomes or contigs. Use for installation, parameter choice, execution, output interpretat...

pku-embl/metagenomics-skills

DAS Tool (Dereplication, Aggregation and Scoring) integrates multiple binning predictions into one non-redundant MAG set for a sin...