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BI
bio-genome-assembly-contamination-detection
Maintainer FreedomIntelligence · Last updated April 1, 2026
Detect and remove contamination in assembled genomes.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-genome-assembly-contamination-detection
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- checkm2 predict --input assembly.fa --output-directory checkm2_output --threads 16.
- checkm2 predict --input genomes/ --output-directory checkm2_output \ --threads 16 --extension fa.
Source Doc
Excerpt From SKILL.md
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
checkm lineage_wf -t 16 -x fa genomes/ checkm_output/
Use cases
- Use bio-genome-assembly-contamination-detection for genomics and bioinformatics workflows.
- Apply bio-genome-assembly-contamination-detection to sequencing, variant, or omics analysis tasks.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- genome-assembly/assembly-qc - BUSCO and other QC
- genome-assembly/long-read-assembly - Assembly methods
- metagenomics/taxonomic-profiling - Metagenome analysis
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