FastQ Screen is a software tool designed for multi-genome mapping and quality control in DNA sequencing analysis. It helps validate the origin of DNA samples by quantifying the proportion of reads that map to a panel of reference genomes. The tool is intended for routine use as a quality control measure and for analyzing samples with uncertain or multiple DNA sources. FastQ Screen uses aligners like Bowtie, Bowtie2, or BWA to map reads against pre-specified genomes and provides both text and graphical outputs to confirm genomic origin or identify contamination. It also reports whether alignments are to unique positions or multiple locations within the genome. FastQ Screen is compatible with various sequencing types, including genomic DNA, RNA-Seq, ChIP-Seq, and Hi-C experiments. It is also compatible with Bismark for processing bisulfite sequence data. The tool has several advantages over similar tools, including direct reporting of multi-mapping reads and the ability to create filtered FASTQ files. It is the only QC tool that aligns reads to multiple bisulfite reference genomes. The software is implemented in Perl and uses the CPAN module GD::Graph for generating summary bar plots. It requires a functional version of Bowtie, Bowtie2, or BWA and should be run on a Linux-based operating system. FastQ Screen has been used in various applications, including preliminary sequencing QC, identifying sample origin, and filtering results. It has been incorporated into bioinformatics workflows and is compatible with MultiQC. FastQ Screen is available from the authors' website and GitHub. It is open-source and distributed under the GNU GPL 3.0 license. The tool has received positive peer review and is recommended for use in sequencing pipelines. It is a valuable tool for researchers working with multiple species samples or aiming to prevent unexpected contamination. The software is well-documented and has been used in various research settings, including the identification of contamination in historical samples.FastQ Screen is a software tool designed for multi-genome mapping and quality control in DNA sequencing analysis. It helps validate the origin of DNA samples by quantifying the proportion of reads that map to a panel of reference genomes. The tool is intended for routine use as a quality control measure and for analyzing samples with uncertain or multiple DNA sources. FastQ Screen uses aligners like Bowtie, Bowtie2, or BWA to map reads against pre-specified genomes and provides both text and graphical outputs to confirm genomic origin or identify contamination. It also reports whether alignments are to unique positions or multiple locations within the genome. FastQ Screen is compatible with various sequencing types, including genomic DNA, RNA-Seq, ChIP-Seq, and Hi-C experiments. It is also compatible with Bismark for processing bisulfite sequence data. The tool has several advantages over similar tools, including direct reporting of multi-mapping reads and the ability to create filtered FASTQ files. It is the only QC tool that aligns reads to multiple bisulfite reference genomes. The software is implemented in Perl and uses the CPAN module GD::Graph for generating summary bar plots. It requires a functional version of Bowtie, Bowtie2, or BWA and should be run on a Linux-based operating system. FastQ Screen has been used in various applications, including preliminary sequencing QC, identifying sample origin, and filtering results. It has been incorporated into bioinformatics workflows and is compatible with MultiQC. FastQ Screen is available from the authors' website and GitHub. It is open-source and distributed under the GNU GPL 3.0 license. The tool has received positive peer review and is recommended for use in sequencing pipelines. It is a valuable tool for researchers working with multiple species samples or aiming to prevent unexpected contamination. The software is well-documented and has been used in various research settings, including the identification of contamination in historical samples.