RT Journal Article
SR Electronic
T1 PaSD-qc: Quality control for single cell whole-genome sequencing data using power spectral density estimation
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 166637
DO 10.1101/166637
A1 Maxwell A. Sherman
A1 Alison R. Barton
A1 Michael Lodato
A1 Carl Vitzthum
A1 Michael E. Coulter
A1 Christopher A. Walsh
A1 Peter J. Park
YR 2017
UL http://biorxiv.org/content/early/2017/07/21/166637.abstract
AB Single cell whole-genome sequencing (scWGS) is providing novel insights into the nature of genetic heterogeneity in normal and diseased cells. However, scWGS introduces DNA amplification-related biases that can confound downstream analysis. Here we present a statistical method, with an accompanying package PaSD-qc (Power Spectral Density-qc), that evaluates the quality of single cell libraries. It uses a modified power spectral density to assess amplification uniformity, amplicon size distribution, autocovariance, and inter-sample consistency as well as identifies aberrantly amplified chromosomes. We demonstrate the usefulness of this tool in evaluating scWGS protocols and in selecting high-quality libraries from low-coverage data for deep sequencing.