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

Nature Methods
Tyler GarvinMichael C Schatz

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.

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Citations

Jan 19, 2016·Molecular Oncology·Ellen HeitzerMichael R Speicher
Apr 19, 2016·Nature Methods·Hamim ZafarKen Chen
Jul 1, 2016·Proceedings of the National Academy of Sciences of the United States of America·Giulio CaravagnaBud Mishra
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Methods Mentioned

BETA
single-cell sequencing
single-cell
fluorescence-activated cell sorting
MDA
FACS
fluorescence activated cell sorting
single
single cell sequencing

Software Mentioned

DOP
bowtie
SAM
CNVnator
PCR
MDA
MALBAC
Ginkgo

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