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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.

GPTomics
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GPTomics
Updated 2/13/2026
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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