bio-metagenomics-kraken
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.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-metagenomics-kraken --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: Kraken2 2.1+, MetaPhlAn 4.1+, pandas 2.2+ 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. # Kraken2 Classification **"Classify what organisms are in my metagenomic sample"** → Assign taxonomic labels to sequencing reads using exact k-mer matching against a reference database for fast initial classification. - CLI: `kraken2 --db db --paired R1.fastq R2.fastq --report report.txt` ## Basic Classification ```bash # Classify reads against standard database kraken2 --db /path/to/kraken2_db \ --output output.kraken \ --report report.txt \ reads.fastq.gz ``` ## Paired-End Reads ```bash kraken2 --db /path/to/kraken2_db \ --paired \ --output output.kraken \ --report report.txt \ reads_R1.fastq.gz reads_R2.fastq.gz ``` ## Common Options ```bash kraken2 --db /path/to/kraken2_db \ --threads 8 \ # CPU threads
- Version Compatibility
- Basic Classification
- Paired-End Reads
- Common Options
- Memory-Efficient Mode
- Report Only (No Per-Read Output)
- Classified/Unclassified Output
- Build Custom Database
- Add Custom Sequences
- Inspect Database
- Report Format
- Parse Kraken Output in Python
- Filter Report by Rank
- Key Parameters
Classify reads against standard database kraken2 --db /path/to/kraken2_db \ reads.fastq.gz reads_R1.fastq.gz reads_R2.fastq.gz For systems with limited RAM Save space by not writing per-read classifications Separate classified and unclassified reads Download taxonomy kraken2-build --download-taxonomy --db custom_db Download specific libraries
What does the bio-metagenomics-kraken skill do?
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.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-metagenomics-kraken --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 FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 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.