PaSD-qc: quality control for single cell whole-genome sequencing data using power spectral density estimation.

ABSTRACT: Single cell whole-genome sequencing (scWGS) is providing novel insights into the nature of genetic heterogeneity in normal and diseased cells. However, the whole-genome amplification process required for scWGS introduces biases into the resulting sequencing that can confound downstream analysis. Here, we present a statistical method, with an accompanying package PaSD-qc (Power Spectral Density-qc), that evaluates the properties and 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 to identify chromosomes with aberrant read-density profiles due either to copy alterations or poor amplification. These metrics provide a standard way to compare the qua

SUBMITTER: Sherman MA 

PROVIDER: S-EPMC5829578 | biostudies-literature | 2018 Feb

REPOSITORIES: biostudies-literature