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Nat Methods. 2015 Nov;12(11):1058-60. doi: 10.1038/nmeth.3578. Epub 2015 Sep 7.

Interactive analysis and assessment of single-cell copy-number variations.

Author information

1
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
2
Department of Molecular and Cellular Biology, Stony Brook University, Stony Brook, 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.

PMID:
26344043
PMCID:
PMC4775251
DOI:
10.1038/nmeth.3578
[Indexed for MEDLINE]
Free PMC Article

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