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