Data & ReproScientific DatabasesFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

bio-metagenomics-kraken

Maintainer FreedomIntelligence · Last updated April 1, 2026

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.

OpenClawNanoClawDiscoveryDataset Buildingbio-metagenomics-kraken🧬 bioinformatics (gptomics bio-* suite)bioinformatics — metagenomics & microbiometaxonomic

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

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

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

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

CLI: kraken2 --db db --paired R1.fastq R2.fastq --report report.txt.
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.
kraken2 --db /path/to/kraken2_db \ --output output.kraken \ --report report.txt \ reads.fastq.gz.

Source Doc

Excerpt From SKILL.md

For systems with limited RAM

kraken2 --db /path/to/kraken2_db
--memory-mapping \ # Use disk-based database --output output.kraken
--report report.txt
reads.fastq.gz


## Save space by not writing per-read classifications

kraken2 --db /path/to/kraken2_db \
    --report report.txt \
    --report-zero-counts \         # Include taxa with 0 counts
    reads.fastq.gz

Separate classified and unclassified reads

kraken2 --db /path/to/kraken2_db
--classified-out classified#.fq \ # # replaced by 1/2 for PE --unclassified-out unclassified#.fq
--output output.kraken
--report report.txt
--paired
reads_R1.fastq.gz reads_R2.fastq.gz