RT Journal Article SR Electronic T1 Interactive analysis and quality assessment of single-cell copy-number variations JF bioRxiv FD Cold Spring Harbor Laboratory SP 011346 DO 10.1101/011346 A1 Tyler Garvin A1 Robert Aboukhalil A1 Jude Kendall A1 Timour Baslan A1 Gurinder S. Atwal A1 James Hicks A1 Michael Wigler A1 Michael C. Schatz YR 2015 UL http://biorxiv.org/content/early/2015/03/06/011346.abstract AB We present an open-source visual-analytics web platform, Ginkgo (http://qb.cshl.edu/ginkgo), for the interactive analysis and quality assessment of single-cell copy-number alterations. Ginkgo automatically constructs copy-number profiles of individual cells from mapped reads, as well as constructing phylogenetic trees of related cells. We validate Ginkgo by reproducing the results of five major studies and examine the data characteristics of three commonly used single-cell amplification techniques to conclude DOP-PCR to be the most consistent for CNV analysis.