FastQ Screen is a tool designed for multi-genome mapping and quality control in DNA sequencing analysis. It addresses the need to map reads against multiple reference genomes to confirm the origin of DNA samples, detect contamination, and identify sample swaps. The tool uses Bowtie², Bowtie 2, or BWA to map reads and provides both text and graphical outputs, allowing users to confirm the genomic origin of samples or identify DNA contamination. FastQ Screen is versatile, suitable for various applications such as genomic DNA, RNA-Seq, ChIP-Seq, and Hi-C experiments, and is compatible with Bismark for processing bisulfite sequence data. It has been used in various studies, including identifying the origin of materials from historical artifacts and clinical microbial metagenomics. The software is available under the GNU GPL 3.0 license and can be accessed via its website and GitHub repository.FastQ Screen is a tool designed for multi-genome mapping and quality control in DNA sequencing analysis. It addresses the need to map reads against multiple reference genomes to confirm the origin of DNA samples, detect contamination, and identify sample swaps. The tool uses Bowtie², Bowtie 2, or BWA to map reads and provides both text and graphical outputs, allowing users to confirm the genomic origin of samples or identify DNA contamination. FastQ Screen is versatile, suitable for various applications such as genomic DNA, RNA-Seq, ChIP-Seq, and Hi-C experiments, and is compatible with Bismark for processing bisulfite sequence data. It has been used in various studies, including identifying the origin of materials from historical artifacts and clinical microbial metagenomics. The software is available under the GNU GPL 3.0 license and can be accessed via its website and GitHub repository.