Data & ReproBioinformatics & GenomicsFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

bio-workflows-metagenomics-pipeline

Maintainer FreedomIntelligence · Last updated April 1, 2026

Metagenomics: QC → classification → functional profiling → AMR.

OpenClawNanoClawAnalysisReproductionbio-workflows-metagenomics-pipeline🧠 bioos extended suitebioos extended bioinformatics suitemetagenomics

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

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

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

Complete workflow from metagenomic FASTQ to taxonomic and functional profiles.
for 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.

Source Doc

Excerpt From SKILL.md

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

Use cases

Use bio-workflows-metagenomics-pipeline for genomics and bioinformatics workflows.
Apply bio-workflows-metagenomics-pipeline to sequencing, variant, or omics analysis tasks.