albert-ying/.autolab/acquired_skills/bracken
.autolab/acquired_skills/bracken/SKILL.md
# Bracken - Bayesian Reestimation of Abundance with KrakEN ## When to Use Use Bracken to estimate species/genus/phylum-level abundances from Kraken2 classification results. ## Standard Workflow 1. Install: `conda install -c bioconda bracken` 2. Run after Kraken2: `bracken -d <db_path> -i <kraken_report.txt> -o <bracken_output.txt> -r <read_length> -l <level> -t <threshold>` 3. Output: abundance table with fraction_total_reads per taxon ## Key Parameters - `-d`: Kraken2 database path (must con
$ install --global
skillsauthnpx skillsauth add albert-ying/autonomous-lab .autolab/acquired_skills/brackenInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
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SKILL.md
Bracken - Bayesian Reestimation of Abundance with KrakEN
When to Use
Use Bracken to estimate species/genus/phylum-level abundances from Kraken2 classification results.
Standard Workflow
- Install:
conda install -c bioconda bracken - Run after Kraken2:
bracken -d <db_path> -i <kraken_report.txt> -o <bracken_output.txt> -r <read_length> -l <level> -t <threshold> - Output: abundance table with fraction_total_reads per taxon
Key Parameters
-d: Kraken2 database path (must contain kmer_distrib files)-i: Kraken2 report file-o: Output file-r: Read length (50, 75, 100, 150, 200, 250, 300)-l: Taxonomic level (S=species, G=genus, F=family, O=order, C=class, P=phylum, K=kingdom, D=domain)-t: Minimum read threshold (default 0)
Key Decisions
- Read length should match the kmer_distrib files available in the database
- Taxonomic level determines granularity of abundance estimates
- The kmer_distrib files (e.g., database150mers.kmer_distrib) are required
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