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. 2018 Aug 24:7:1338.
doi: 10.12688/f1000research.15931.2. eCollection 2018.

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

Steven W Wingett  1 , Simon Andrews  1
Affiliations

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

Steven W Wingett et al. F1000Res. .

Abstract

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.

Keywords: Bioinformatics Contamination FastQC Illumina Metagenomics NGS QC Sequencing.

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Conflict of interest statement

No competing interests were disclosed.

Figures

Figure 1.
Figure 1.. Graphical output from FastQ Screen after mapping a publicly available RNA-Seq sample (SRR5100711) against several reference genomes.
Reads either i) mapped uniquely to one genome only (light blue), ii) multi-mapped to one genome only (dark blue), iii) mapped uniquely to a given genome and mapped to at least one other genome (light red), or iv) multi-mapped to a given genome and mapped to at least one other genome (dark red). The reads represented by blue shading are significant since these are sequences that align only to one genome, and consequently, if are observed in an unexpected genome they suggest contamination.
See this image and copyright information in PMC

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References

    1. Langmead B, Trapnell C, Pop M, et al. : Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10(3):R25. 10.1186/gb-2009-10-3-r25 - DOI - PMC - PubMed
    1. Langmead B, Salzberg SL: Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357–359. 10.1038/nmeth.1923 - DOI - PMC - PubMed
    1. Li H, Durbin R: Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25(14):1754–1760. 10.1093/bioinformatics/btp324 - DOI - PMC - PubMed
    1. Woodham EF, Paul NR, Tyrrell B, et al. : Coordination by Cdc42 of Actin, Contractility, and Adhesion for Melanoblast Movement in Mouse Skin. Curr Biol. 2017;27(5):624–637. 10.1016/j.cub.2017.01.033 - DOI - PMC - PubMed
    1. Krueger F, Andrews SR: Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics. 2011;27(11):1571–1572. 10.1093/bioinformatics/btr167 - DOI - PMC - PubMed

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