数据与复现生物信息与基因组学FreedomIntelligence/OpenClaw-Medical-Skills数据与复现

bio-workflows-metagenomics-pipeline

维护者 FreedomIntelligence · 最近更新 2026年4月1日

Metagenomics: QC → classification → functional profiling → AMR.

OpenClawNanoClaw分析处理复现实验bio-workflows-metagenomics-pipeline🧠 bioos extended suitebioos extended bioinformatics suitemetagenomics

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-workflows-metagenomics-pipeline

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

2 min

核心说明

Complete workflow ，面向 metagenomic FASTQ to taxonomic 、 functional profiles。
用于 sample in sample1 sample2 sample3；do fastp -i ${sample}_R1.fastq.gz -I ${sample}_R2.fastq.gz \ -o trimmed/${sample}_R1.fq.gz -O trimmed/${sample}_R2.fq.gz \ --detect_adapter_for_pe \ --qualified_quality_phred 20 \ --length_required 50 \ --html qc/${sample}_fastp.html done。

原始文档

SKILL.md 摘录

Remove host reads (human example)

for sample in sample1 sample2 sample3; do bowtie2 -p 8 -x human_index
-1 trimmed/${sample}_R1.fq.gz
-2 trimmed/${sample}_R2.fq.gz
--un-conc-gz host_removed/${sample}_R%.fq.gz
> /dev/null 2> qc/${sample}_host_removal.log done


## Classify reads

for sample in sample1 sample2 sample3; do
    kraken2 --db kraken2_db \
        --threads 8 \
        --paired \
        --report kraken/${sample}.report \
        --output kraken/${sample}.output \
        host_removed/${sample}_R1.fq.gz \
        host_removed/${sample}_R2.fq.gz
done

Estimate species abundance

for sample in sample1 sample2 sample3; do bracken -d kraken2_db
-i kraken/${sample}.report
-o bracken/${sample}.species.txt
-r 150
-l S
-t 10 done

适用场景

Use bio-workflows-metagenomics-pipeline ，用于 genomics 、 bioinformatics workflows。
Apply bio-workflows-metagenomics-pipeline to sequencing，variant，或 omics analysis tasks。