bio-read-qc-contamination-screening
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.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-read-qc-contamination-screening --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: BBTools 39.0+, Bowtie2 2.5.3+, FastQ Screen 0.15+, FastQC 0.12+, MultiQC 1.21+ Before using code patterns, verify installed versions match. If versions differ: - 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 Screening 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 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 ## Basic Usage ```bash # Screen against configured genomes fastq_screen sample.fastq.gz # Multiple files fastq_screen *.fastq.gz # Specify output directory fastq_screen --outdir qc_results/
- Version Compatibility
- FastQ Screen Overview
- Basic Usage
- Configuration File
- Pre-built Databases
- Screening Options
- Output Options
- Filter Codes
- Output Files
- Results Format
- Interpreting Results
- Expected Results by Sample Type
- Common Issues
- MultiQC Integration
Screen against configured genomes fastq_screen sample.fastq.gz Multiple files fastq_screen *.fastq.gz Specify output directory fastq_screen --outdir qc_results/ sample.fastq.gz Custom config file fastq_screen --conf my_screen.conf sample.fastq.gz Download common screening databases fastq_screen --get_genomes
What does the bio-read-qc-contamination-screening skill do?
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.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-read-qc-contamination-screening --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.