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

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.

Single-Cell Analysis Reveals Heterogeneity of High Endothelial Venules and Different Regulation of Genes Controlling Lymphocyte Entry to Lymph Nodes

“…To filter low quality sequences and cells, fractions of reads mapping to the mouse genome, spike-in controls and mitochondrial genes were calculated for each cell. To filter low quality samples, FASTQ files were first analyzed using fastqscreen v0.9.5 (Wingett and Andrews, 2018) for non-murine contaminants. Then FASTQC v0.11.2 was run on samples before and after trimming to evaluate quality of reads and adaptor contamination.…”

Functional Dominance of CHIP-Mutated Hematopoietic Stem Cells in Patients Undergoing Autologous Transplantation

“…For the PPM1D and TruSight Myeloid Panel libraries, read quality was assessed using FastQC (Wingett and Andrews, 2018). Subsequently, reads were mapped to the hg19 draft of the human genome using BWA-MEM (Li and Durbin, 2009).…”

Global transcriptomic profiling of the bone marrow stromal microenvironment during postnatal development, aging and inflammation

“…The quality of the raw data was assessed using FastQC v0.11.3 (Andrews, 2010) and FastQ Screen v0.5.2 (Wingett and Andrews, 2018) tools. Cutadapt (Martin, 2011) was used to remove the adaptors, trim the first three bases of the reads and the 3' and 5' end nucleotides with a quality cutoff of 20, requiring a minimum length of 40.…”