bio-metagenomics-abundance
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.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-metagenomics-abundance --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: Bracken 2.9+, 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. # Abundance Estimation with Bracken **"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` ## Basic Abundance Estimation ```bash # Run Bracken on Kraken2 report 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 ``` ## Full Workflow with Kraken2 ```bash # Step 1: Classify with Kraken2 kraken2 --db /path/to/kraken2_db \ --threads 8 \ --paired \ --report sample_kraken_report.t
- Version Compatibility
- Basic Abundance Estimation
- Full Workflow with Kraken2
- Different Taxonomic Levels
- Build Bracken Database
- Output Format
- Filter Low-Abundance Taxa
- Combine Multiple Samples
- Parse Bracken Output in Python
- Convert to Relative Abundance
- Create Abundance Matrix
- Key Parameters
- Taxonomic Levels
- Read Length Options
Run Bracken on Kraken2 report bracken -d /path/to/kraken2_db \ Step 1: Classify with Kraken2 kraken2 --db /path/to/kraken2_db \ reads_R1.fastq.gz reads_R2.fastq.gz Step 2: Estimate abundances with Bracken Species level (default) bracken -d db -i report.txt -o species.txt -r 150 -l S Genus level bracken -d db -i report.txt -o genus.txt -r 150 -l G
What does the bio-metagenomics-abundance skill do?
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.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-metagenomics-abundance --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.