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Updated: Apr 4, 2026

Detection of Copy Number Alterations Using Single Cell Sequencing
Published on: February 17, 2017
Interactive analysis and assessment of single-cell copy-number variations
Tyler Garvin1, Robert Aboukhalil1, Jude Kendall1
1Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
Abstract:
We present Ginkgo (http://qb.cshl.edu/ginkgo), a user-friendly, open-source web platform for the analysis of single-cell copy-number variations (CNVs). Ginkgo automatically constructs copy-number profiles of cells from mapped reads and constructs phylogenetic trees of related cells. We validated Ginkgo by reproducing the results of five major studies. After comparing three commonly used single-cell amplification techniques, we concluded that degenerate oligonucleotide-primed PCR is the most consistent for CNV analysis.

