bio-read-qc-contamination-screening
Contamination Screening
Screen FASTQ files against multiple genomes to identify contamination sources using FastQ Screen.
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
# Screen against configured genomes
fastq_screen sample.fastq.gz
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