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BI
bio-metagenomics-abundance
Maintainer FreedomIntelligence · Last updated April 1, 2026
Species abundance estimation using Bracken with Kraken2 output. Redistributes reads from higher taxonomic levels to species for more accurate estimates. Use when accurate species-level abundances are needed from Kraken2 classification output.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-metagenomics-abundance
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- CLI: bracken -d db -i kraken2.report -o bracken.output -r 150 -l S.
- Get species-level abundances from my Kraken2 results" → Redistribute reads assigned to higher taxonomic levels down to species using Bracken's Bayesian re-estimation for more accurate abundance profiles. CLI: bracken -d db -i kraken2.report -o bracken.output -r 150 -l S.
- bracken -d /path/to/kraken2_db \ -i kraken_report.txt \ -o bracken_output.txt \ -r 150 \ # Read length (100, 150, 200, 250, 300) -l S # Taxonomic level.
Source Doc
Excerpt From SKILL.md
Step 1: Classify with Kraken2
kraken2 --db /path/to/kraken2_db
--threads 8
--paired
--report sample_kraken_report.txt
reads_R1.fastq.gz reads_R2.fastq.gz
Step 2: Estimate abundances with Bracken
bracken -d /path/to/kraken2_db
-i sample_kraken_report.txt
-o sample_bracken_species.txt
-w sample_bracken_report.txt
-r 150
-l S
## Species level (default)
bracken -d db -i report.txt -o species.txt -r 150 -l S
Use cases
- Use when accurate species-level abundances are needed from Kraken2 classification output.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- kraken-classification - Generate Kraken2 report
- metaphlan-profiling - Alternative profiling method
- metagenome-visualization - Visualize abundances
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