「metagenomics」の検索結果

End-to-end shotgun metagenomics workflow from FASTQ to taxonomic and functional profiles, orchestrating controls/host depletion, Kraken2+Bracken classification, MetaPhlAn marker profiling, and HUMAnN functional profiling. Covers the controls-first ordering, why Kraken2 read counts are not abundances and MetaPhlAn cell fractions do not equal Bracken read fractions, and the consistent-pipeline framing. Use when profiling shotgun metagenomic samples end to end, or chaining classification, abundance, and function. For resistome see metagenomics/amr-detection; for strains see metagenomics/strain-tracking; for assembly see genome-assembly/metagenome-assembly.

日本語の概要は準備中です。原文の説明を表示しています。

Kick off public shotgun metagenomics QC, host-depletion, taxonomic profiling, and functional profiling workflows using nf-core/taxprofiler, Kraken2, Bracken, MetaPhlAn, and HUMAnN.

日本語の概要は準備中です。原文の説明を表示しています。

Shotgun metagenomics workflow with host-depletion-aware QC, taxonomic profiling, functional profiling, AMR follow-up, and reproducible community output tables.

日本語の概要は準備中です。原文の説明を表示しています。

Discover and invoke 1,676 deduplicated biomedical AI agent skills from the Awesome Bio Agent Skills repository (20 source repos, 15 categories). Use this skill as a router whenever a user needs a bioinformatics/biomedical task (genomics, transcriptomics, single-cell, proteomics, protein design, clinical, epigenomics, multi-omics, pathway, metagenomics, database queries, visualization, workflows): search the index, locate the best-matching skill, fetch its SKILL.md, and follow it.

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METAINFORMANT rules for directory src/metainformant/metagenomics/diversity. Use when editing, adding tests, or reviewing code under this path. Read the linked AGENTS.md first; use uv only, write outputs to output/, real implementations.

日本語の概要は準備中です。原文の説明を表示しています。

METAINFORMANT rules for directory src/metainformant/metagenomics/comparative. Use when editing, adding tests, or reviewing code under this path. Read the linked AGENTS.md first; use uv only, write outputs to output/, real implementations.

日本語の概要は準備中です。原文の説明を表示しています。

METAINFORMANT rules for directory src/metainformant/metagenomics/amplicon. Use when editing, adding tests, or reviewing code under this path. Read the linked AGENTS.md first; use uv only, write outputs to output/, real implementations.

日本語の概要は準備中です。原文の説明を表示しています。

METAINFORMANT rules for directory src/metainformant/metagenomics. Use when editing, adding tests, or reviewing code under this path. Read the linked AGENTS.md first; use uv only, write outputs to output/, real implementations.

日本語の概要は準備中です。原文の説明を表示しています。

METAINFORMANT rules for directory src/metainformant/metagenomics/visualization. Use when editing, adding tests, or reviewing code under this path. Read the linked AGENTS.md first; use uv only, write outputs to output/, real implementations.

日本語の概要は準備中です。原文の説明を表示しています。

METAINFORMANT rules for directory src/metainformant/metagenomics/shotgun. Use when editing, adding tests, or reviewing code under this path. Read the linked AGENTS.md first; use uv only, write outputs to output/, real implementations.

日本語の概要は準備中です。原文の説明を表示しています。

METAINFORMANT rules for directory src/metainformant/metagenomics/functional. Use when editing, adding tests, or reviewing code under this path. Read the linked AGENTS.md first; use uv only, write outputs to output/, real implementations.

日本語の概要は準備中です。原文の説明を表示しています。

METAINFORMANT rules for directory docs/metagenomics. Use when editing, adding tests, or reviewing code under this path. Read the linked AGENTS.md first; use uv only, write outputs to output/, real implementations.

日本語の概要は準備中です。原文の説明を表示しています。

Species abundance estimation using Bracken with Kraken2 output. Redistributes reads from higher taxonomic levels to species for more accurate estimates. Use when accurate species-level abundances are needed from Kraken2 classification output.

日本語の概要は準備中です。原文の説明を表示しています。

Taxonomic classification of metagenomic reads using Kraken2. Fast k-mer based classification against RefSeq database. Use when performing initial taxonomic classification of shotgun metagenomic reads before abundance estimation with Bracken.

日本語の概要は準備中です。原文の説明を表示しています。

Track bacterial strains using MASH, sourmash, fastANI, and inStrain. Compare genomes, detect contamination, and monitor strain-level variation. Use when needing sub-species resolution for outbreak tracking, transmission analysis, or within-host strain dynamics.

日本語の概要は準備中です。原文の説明を表示しています。

Marker gene-based taxonomic profiling using MetaPhlAn 4. Provides accurate species-level relative abundances using clade-specific markers. Use when accurate taxonomic profiling is needed and computational resources are limited, or for comparison with HMP/other MetaPhlAn studies.

日本語の概要は準備中です。原文の説明を表示しています。

Profile functional potential of metagenomes using HUMAnN3 and similar tools. Use when obtaining pathway abundances, gene family counts, or functional annotations from metagenomic data.

日本語の概要は準備中です。原文の説明を表示しています。

Visualize metagenomic profiles using R (phyloseq, microbiome) and Python (matplotlib, seaborn). Create stacked bar plots, heatmaps, PCA plots, and diversity analyses. Use when creating publication-quality figures from MetaPhlAn, Bracken, or other taxonomic profiling output.

日本語の概要は準備中です。原文の説明を表示しています。

Predict metagenome functional content from 16S rRNA marker gene data using PICRUSt2. Infer KEGG, MetaCyc, and EC abundances from ASV tables. Use when functional profiling is needed from 16S data without shotgun metagenomics sequencing.

日本語の概要は準備中です。原文の説明を表示しています。

Detect antimicrobial resistance genes using AMRFinderPlus, ResFinder, and CARD. Screen isolates and metagenomes for resistance determinants. Use when characterizing resistance profiles in clinical isolates, surveillance samples, or metagenomic data.

日本語の概要は準備中です。原文の説明を表示しています。

Installs 425 bioinformatics skills covering sequence analysis, RNA-seq, single-cell, variant calling, metagenomics, structural biology, and 56 more categories. Use when setting up bioinformatics capabilities or when a bioinformatics task requires specialized skills not yet installed.

日本語の概要は準備中です。原文の説明を表示しています。

Think and work like an expert Microbiologist. Use when a task calls for Microbiologist judgment. Reasons from culturability limits, CFU/MPN enumeration, selective media, DADA2/QIIME2 16S ASVs (SILVA/GTDB), and shotgun metagenomics (Kraken2, MetaPhlAn, HUMAnN); treats plate-count anomaly, compositional stats pitfalls, kit contamination, and index hopping as first-class failure modes.

日本語の概要は準備中です。原文の説明を表示しています。

Installs 425 bioinformatics skills covering sequence analysis, RNA-seq, single-cell, variant calling, metagenomics, structural biology, and 56 more categories. Use when setting up bioinformatics capabilities or when a bioinformatics task requires specialized skills not yet installed.

日本語の概要は準備中です。原文の説明を表示しています。

Detect antimicrobial resistance genes using AMRFinderPlus, ResFinder, and CARD. Screen isolates and metagenomes for resistance determinants. Use when characterizing resistance profiles in clinical isolates, surveillance samples, or metagenomic data.

日本語の概要は準備中です。原文の説明を表示しています。