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

Concepts

Life SciencesBiologyGeneticsComparative GenomicsGenomic Data AnalysisGenomicsDna SequencingGenome MappingGenome SequencingNext-generation SequencingRead MappingSequence Quality ControlPaired-end Read MappingRead Mapping Quality ControlRead Mapping ValidationReference Genome Mapping

TL;DR

DNA sequencing usually maps reads to a single reference genome, but mapping to multiple genomes is needed to confirm origin, detect contamination, or identify sample swaps. FastQ Screen was developed 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 for routine quality control and for analysing samples with uncertain or multiple DNA origins.

Abstract

<ns3:p>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.</ns3:p>