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数据与复现
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bio-metagenomics-functional-profiling
维护者 FreedomIntelligence · 最近更新 2026年4月1日
Profile functional potential of metagenomes using HUMAnN3 and similar tools. Use when obtaining pathway abundances, gene family counts, or functional annotations from metagenomic data.
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-metagenomics-functional-profiling
- 维护者
- FreedomIntelligence
- 许可
- MIT
- 最近更新
- 2026年4月1日
技能摘要
来自 SKILL.md 的关键信息
核心说明
- CLI：humann --input reads.fastq --output results/ (HUMAnN3)。
- What metabolic pathways are present in my metagenome?" → Profile functional potential of metagenomic samples to obtain pathway abundances 、 gene family counts ，使用 translated search against UniRef 、 MetaCyc. CLI：humann --input reads.fastq --output results/ (HUMAnN3)。
- Profile functional potential of metagenomic samples ，使用 HUMAnN3 to get pathway 、 gene family abundances。
- conda create -n humann -c bioconda humann conda activate humann。
原始文档
SKILL.md 摘录
Download databases
humann_databases --download chocophlan full /path/to/databases humann_databases --download uniref uniref90_diamond /path/to/databases
Update config with database paths
humann_config --update database_folders nucleotide /path/to/databases/chocophlan humann_config --update database_folders protein /path/to/databases/uniref
## Run HUMAnN3 on a single sample
humann --input sample.fastq.gz --output sample_humann
适用场景
- 适合在obtaining pathway abundances，gene family counts，或 functional annotations ，面向 metagenomic data时使用。
不适用场景
- Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。
上游相关技能
- metagenomics/metaphlan-profiling - Taxonomic profiling (input for HUMAnN)
- metagenomics/kraken-classification - Alternative taxonomy
- metagenomics/metagenome-visualization - Visualization methods
- pathway-analysis/kegg-pathways - KEGG pathway interpretation
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