bio-genome-assembly-contamination-detection
Detect contamination and assess genome quality using CheckM, CheckM2, GTDB-Tk, and GUNC for metagenome-assembled genomes and isolate assemblies. Use when checking assemblies for contamination.
npx skills add BioTender-max/awesome-bio-agent-skills --skill contamination-detection --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: 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. # Contamination Detection **"Check my assembly for contamination"** → Evaluate genome completeness and detect contaminating sequences using marker gene sets or chimeric contig detection. - CLI: `checkm2 predict --input assembly.fa`, `gunc run`, `gtdbtk classify_wf` ## CheckM2 (Recommended) ```bash # Run CheckM2 on single genome checkm2 predict --input assembly.fa --output-directory checkm2_output --threads 16 # Run on multiple genomes (directory of FASTAs) checkm2 predict --input genomes/ --output-directory checkm2_output \ --threads 16 --extension fa # Output: quality_report.tsv with Completeness, Contamination, Coding_Density ``` ## Interpret CheckM2 Results ```bash # quality_report.tsv columns: # Name, Completeness, Contamination, Com
- Version Compatibility
- CheckM2 (Recommended)
- Interpret CheckM2 Results
- CheckM (Original)
- CheckM Plots
- GTDB-Tk Taxonomic Classification
- GTDB-Tk De Novo Workflow
- GUNC Chimerism Detection
- GUNC Interpretation
- Comprehensive QC Pipeline
- Filter by Quality Standards
- Remove Contamination
- Detect Foreign Contigs
- Decontaminate with BlobTools
Run CheckM2 on single genome checkm2 predict --input assembly.fa --output-directory checkm2_output --threads 16 Run on multiple genomes (directory of FASTAs) checkm2 predict --input genomes/ --output-directory checkm2_output \ quality_report.tsv columns: Filter high-quality genomes (MIMAG standards) awk -F'\t' 'NR==1 || ($2 > 90 && $3 < 5)' quality_report.tsv > high_quality_mags.tsv Medium quality awk -F'\t' 'NR==1 || ($2 >= 50 && $3 < 10)' quality_report.tsv > medium_quality_mags.tsv Run CheckM lineage workflow
What does the bio-genome-assembly-contamination-detection skill do?
Detect contamination and assess genome quality using CheckM, CheckM2, GTDB-Tk, and GUNC for metagenome-assembled genomes and isolate assemblies. Use when checking assemblies for contamination.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill contamination-detection --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 BioTender-max/awesome-bio-agent-skills, a repository with 135 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.