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bio-read-qc-contamination-screening
Maintainer FreedomIntelligence · Last updated April 1, 2026
Detect sample contamination and cross-species reads using FastQ Screen. Screen reads against multiple reference genomes to identify bacterial, viral, adapter, or sample swap contamination. Use when suspecting cross-contamination or working with samples prone to microbial contamination.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-read-qc-contamination-screening
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- CLI: fastq_screen --conf fastq_screen.conf reads.fq.
- Screen FASTQ files against multiple genomes to identify contamination sources using FastQ Screen.
- Check for contamination in sequencing data" → Align a sample of reads against multiple reference genomes to identify cross-species or cross-sample contamination. CLI: fastq_screen --conf fastq_screen.conf reads.fq.
- fastq_screen sample.fastq.gz.
Source Doc
Excerpt From SKILL.md
FastQ Screen Overview
FastQ Screen aligns a subset of reads against multiple reference genomes to identify:
- Cross-species contamination
- Bacterial/viral contamination
- Adapter sequences
- PhiX spike-in
- Sample swaps
Specify output directory
fastq_screen --outdir qc_results/ sample.fastq.gz
Custom config file
fastq_screen --conf my_screen.conf sample.fastq.gz
Use cases
- Use when suspecting cross-contamination or working with samples prone to microbial contamination.
Not for
- Do not treat this catalog entry as a substitute for the full upstream workflow.
Upstream Related Skills
- quality-reports - FastQC shows overrepresented sequences
- adapter-trimming - Remove adapter contamination
- metagenomics/kraken-classification - Deeper taxonomic analysis
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