home/categories/lab-tools/mdbabumiamssm-llms-universal-life-science-and-clinical-skills-skills-ngs-qc-read-qc-contamination-screening-skill-md
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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.
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mdbabumiamssm
Updated 2/4/2026
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quick start
Installation and usage
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.
Installation
$ install --globalskills.sh
Usage
Once installed, you can use this skill by running the following command in your terminal:
skills use bio-read-qc-contamination-screening