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このリポジトリの skills
SkillsMP は PKU-EMBL/Metagenomics-Skills から 163 件の skill を収集しています。skill を開くとソースと詳細を確認できます。
PKU-EMBL/Metagenomics-Skills収集済み skill 163 件中 40 件を表示しています。
PhyloPhlAn 3 — precise phylogenetic analysis of microbial isolates and metagenome-assembled genomes via marker sets, alignment, and tree building. Use when: (1) Reconstructing phylogenies across many MAGs/genomes, (2) Contextualizing novel lineages beyond a…
原文の言語: 英語
MMseqs2 — ultra-fast protein sequence search, clustering (Linclust), and contig taxonomy (Steinegger / Söding labs). Use when: (1) Building NR gene catalogues, (2) Sensitive BLASTP-scale search at metagenome size, (3) Contig taxonomy via easy-taxonomy /…
原文の言語: 英語
AlphaGEM — genome-scale metabolic modelling aided by protein structure alignment and deep-learning dark-metabolism mining. Use when: (1) Building or refining GEMs beyond sequence-only gap filling, (2) Integrating structure signals into metabolic networks, (3)…
原文の言語: 英語
Anvi'o — interactive multi-omics platform for metagenomic assemblies, MAG refinement, visualization, and SNP/profile exploration. Use when: (1) Manual or human-guided bin refinement, (2) Interactive contig profiles across samples, (3) Linking MAGs with…
原文の言語: 英語
Rapid standardized annotation of bacterial genomes (alignment-free ID). Use this skill when working with bakta: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/oschwengers/bakta. For…
原文の言語: 英語
Basic rapid ribosomal RNA predictor for genomes. Use this skill when working with barrnap: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/tseemann/barrnap. For stage routing use…
原文の言語: 英語
Fast splice-aware aligner and BBTools suite utilities (BBMerge, etc.). Use this skill when working with bbmap: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://sourceforge.net/projects/bbmap/. For…
原文の言語: 英語
Benchmarking Universal Single-Copy Orthologs for genome completeness. Use this skill when working with busco: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://gitlab.com/ezlab/busco. For stage…
原文の言語: 英語
Burrows–Wheeler short-read alignment (BWA-MEM) to contigs/genomes. Use this skill when working with bwa: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/lh3/bwa. For stage routing use…
原文の言語: 英語
Quality assessment of metagenome-assembled viral genomes. Use this skill when working with checkv: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://bitbucket.org/berkeleylab/checkv. For routing…
原文の言語: 英語
Composition and coverage binning of metagenomic contigs. Use this skill when working with concoct: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/BinPro/CONCOCT. For stage routing use…
原文の言語: 英語
Adapter/primer trimming for short and long reads. Use this skill when working with cutadapt: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/marcelm/cutadapt. For stage routing use…
原文の言語: 英語
Orthology-based functional annotation (COG/KEGG/CAZy via eggNOG). Use this skill when working with eggnog-mapper: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/eggnogdb/eggnog-mapper.…
原文の言語: 英語
QC reports for Illumina FASTQ before/after trimming. Use this skill when working with fastqc: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/s-andrews/FastQC. For stage routing use…
原文の言語: 英語
Predict bacterial metabolic pathways and reconstruct genome-scale metabolic models. Use this skill when working with gapseq: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream:…
原文の言語: 英語
Fast sensitive taxonomic classification via protein-level matches. Use this skill when working with kaiju: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/bioinformatics-centre/kaiju.…
原文の言語: 英語
Quality thresholds after binning (completeness/contamination, dRep ANI, publication vs refinement gates). Use this skill when: (1) Setting filters for bins before calling them MAGs, (2) Choosing dRep ANI cutoffs, (3) Interpreting CheckM2 reports, (4)…
原文の言語: 英語
Automated multi-metagenome contig binning. Use this skill when working with maxbin2: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://sourceforge.net/projects/maxbin2/. For stage routing use…
原文の言語: 英語
Long-read metagenome assembly with Flye/metaFlye. Use this skill when working with metaflye: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/fenderglass/Flye. For stage routing use…
原文の言語: 英語
High-quality metagenome assembly from long accurate reads. Use this skill when working with metamdbg: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/GaetanBenoitDev/metaMDBG. For stage…
原文の言語: 英語
Fast pairwise alignment for long reads and genome-to-genome maps. Use this skill when working with minimap2: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/lh3/minimap2. For stage…
原文の言語: 英語
Rapid prokaryotic genome annotation (CDS/rRNA/tRNA). Use this skill when working with prokka: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/tseemann/prokka. For stage routing use…
原文の言語: 英語
Assembly quality assessment (contiguity, misassemblies; metaQUAST for metagenomes). Use this skill when working with quast: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/ablab/quast.…
原文の言語: 英語
Fast quantification of gene/transcript abundance; use --meta for metagenomes. Use this skill when working with salmon: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream:…
原文の言語: 英語
Flexible Illumina adapter/quality trimmer. Use this skill when working with trimmomatic: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/usadellab/Trimmomatic. For stage routing use…
原文の言語: 英語
AAMB / AVAMB — adversarial autoencoder metagenomic binning and its ensemble with VAMB for improved near-complete MAG recovery. Use when: (1) Running AAMB as a DL single binner, (2) AVAMB ensemble (VAMB+AAMB) for extra NC genomes, (3) Diversifying bins before…
原文の言語: 英語
Bin Chicken — targeted coassembly planning for recovering low-abundance / novel MAGs by grouping metagenomes that share marker-gene signal (SingleM). Use when: (1) Public or large cohorts where all-vs-all coassembly is impossible, (2) Prioritizing sample…
原文の言語: 英語
CAMI / CAMI II metagenome benchmarking datasets and evaluation stack (CAMISIM, AMBER, OPAL, CAMI Benchmarking Portal). Use when: (1) Downloading CAMI challenge data / gold standards, (2) Choosing marine, plant-associated, strain-madness, mouse-gut, or human…
原文の言語: 英語
Deepurify — multi-modal deep language model for MAG decontamination by matching contigs to taxonomic lineages and splitting chimeric bins into higher-quality sub-MAGs. Use when: (1) Cleaning contaminated MAGs after binning, (2) Rescuing near-threshold…
原文の言語: 英語
FastANI — alignment-free approximate mapping for high-throughput average nucleotide identity (ANI) among prokaryotic genomes/MAGs. Use when: (1) Reproducing literature that reports FastANI, (2) Pairwise/species-boundary ANI at moderate catalogue scales, (3)…
原文の言語: 英語
InSilicoSeq — simulate realistic Illumina (meta)genomic reads for benchmarking and experimental design. Use when: (1) Generating Illumina-like test sets from genomes, (2) Simple abundance-controlled mock communities, (3) Complementing CAMISIM for CAMI-style…
原文の言語: 英語
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)…
原文の言語: 英語
PlasMAAG — recover plasmids and cellular genomes from metagenomes using assembly–alignment graphs and contrastive learning across samples. Use when: (1) Plasmid MAG reconstruction beyond circular-path assemblers, (2) Improving plasmid contig classification vs…
原文の言語: 英語
SingleM — species-level metagenome profiling from conserved windows in universal marker genes, including lineages without genomic representation; Sandpiper aggregates public SingleM profiles. Use when: (1) Profiling environmental communities rich in unknowns,…
原文の言語: 英語
Fast robust average nucleotide identity (ANI) for metagenomic genomes and MAG comparisons. Use for species-level clustering, novelty vs GTDB/UHGG, and scalable ANI matrices. Upstream: https://github.com/bluenote-1577/skani.
原文の言語: 英語
TaxVAMB — semisupervised bimodal VAE binning that integrates TNF, coabundance, and contig taxonomy for improved MAG recovery (incl. incomplete genomes and long-read sets). Use when: (1) Taxonomy-informed binning, (2) Comparing to VAMB/AAMB/SemiBin2, (3)…
原文の言語: 英語
vConTACT2 / vConTACT3 — gene-sharing network and ML-based hierarchical virus taxonomy for prokaryotic (and in v3, broader realm) viral genomes/contigs. Use after viral discovery (geNomad / VirSorter2) and quality (CheckV): (1) Genus-to-order style clustering,…
原文の言語: 英語
Virtual Metabolic Human (VMH) database — human and gut microbiome metabolism integrated with nutrition and disease knowledge for GEM interpretation. Use when: (1) Contextualizing gapseq / AGORA-style models, (2) Linking metabolites, microbes, and nutrition,…
原文の言語: 英語
Use the Genome Taxonomy Database (GTDB) public releases — taxonomy tables, trees, metadata, and representative genomes. Use this skill when: (1) Choosing or citing a GTDB release, (2) Downloading bac120/ar53 taxonomy or reps, (3) Distinguishing GTDB data…
原文の言語: 英語
KEGG as a reference for gene/protein annotation — KO orthologs, pathways, modules, BRITE (BlastKOALA / GhostKOALA and related assignment). Use when: (1) Mapping genes/MAGs to KEGG Orthology, (2) Reconstructing pathways/modules, (3) Choosing KEGG vs eggNOG /…
原文の言語: 英語