bio-workflows-metagenomics-pipeline
End-to-end metagenomics workflow from FASTQ to taxonomic and functional profiles. Covers Kraken2 classification, Bracken abundance estimation, and HUMAnN functional profiling. Use when profiling metagenomic samples.
npx skills add BioTender-max/awesome-bio-agent-skills --skill metagenomics-pipeline --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: Bowtie2 2.5.3+, Bracken 2.9+, HUMAnN 3.8+, Kraken2 2.1+, MetaPhlAn 4.1+, fastp 0.23+, matplotlib 3.8+, pandas 2.2+, seaborn 0.13+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Metagenomics Pipeline **"Analyze my metagenomic samples from FASTQ to taxonomic and functional profiles"** → Orchestrate host depletion, Kraken2/Bracken taxonomic classification, MetaPhlAn profiling, HUMAnN3 functional analysis, and AMR gene detection. Complete workflow from metagenomic FASTQ to taxonomic and functional profiles. ## Workflow Overview ``` FASTQ files | v [1. QC & Host Removal] --> fastp + Bowtie2 | v [2. Taxonomic Classification] | +---> Kraken2 + Bracken (fast, database-dependent) | +---> MetaPhlAn (marker-based, standardized) | v [3. Functional Profiling] --> HUMAnN | v Taxonomic profiles + Pathway abu
- Version Compatibility
- Workflow Overview
- Primary Path: Kraken2 + Bracken + HUMAnN
- Step 1: Quality Control and Host Removal
- Step 2A: Kraken2 Classification
- Step 2B: Bracken Abundance Estimation
- Step 2C: Alternative - MetaPhlAn Profiling
- Step 3: Functional Profiling with HUMAnN
- Visualization
- Parameter Recommendations
- Troubleshooting
- Complete Pipeline Script
- Related Skills
QC with fastp
for sample in sample1 sample2 sample3; do
fastp -i ${sample}_R1.fastq.gz -I ${sample}_R2.fastq.gz \
done
Remove host reads (human example)
bowtie2 -p 8 -x human_index \
Classify reads
kraken2 --db kraken2_db \
Estimate species abundance
bracken -d kraken2_db \What does the bio-workflows-metagenomics-pipeline skill do?
End-to-end metagenomics workflow from FASTQ to taxonomic and functional profiles. Covers Kraken2 classification, Bracken abundance estimation, and HUMAnN functional profiling. Use when profiling metagenomic samples.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill metagenomics-pipeline --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.