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Version 2. F1000Res. 2018 Aug 24 [revised 2018 Sep 17];7:1338. doi: 10.12688/f1000research.15931.2. eCollection 2018.

FastQ Screen: A tool for multi-genome mapping and quality control.

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Bioinformatics, Babraham Institute, Cambridge, CB22 3AT, UK.


DNA sequencing analysis typically involves mapping reads to just one reference genome. Mapping against multiple genomes is necessary, however, when the genome of origin requires confirmation. Mapping against multiple genomes is also advisable for detecting contamination or for identifying sample swaps which, if left undetected, may lead to incorrect experimental conclusions. Consequently, we present FastQ Screen, a tool to validate the origin of DNA samples by quantifying the proportion of reads that map to a panel of reference genomes. FastQ Screen is intended to be used routinely as a quality control measure and for analysing samples in which the origin of the DNA is uncertain or has multiple sources.


Bioinformatics Contamination FastQC Illumina Metagenomics NGS QC Sequencing

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