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bioRxiv · 10.1101/166637

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

Sherman, M. A.·Barton, A. R.·Lodato, M.·Vitzthum, C.·Coulter, M.·Walsh, C.·Park, P.
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Abstract

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.

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Sherman, M. A., Barton, A. R., Lodato, M., Vitzthum, C., Coulter, M., Walsh, C., Park, P.. 2017-07-21. PaSD-qc: Quality control for single cell whole-genome sequencing data using power spectral density estimation. https://doi.org/10.1101/166637

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