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

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.

SUBMITTER: Garvin T 

PROVIDER: S-EPMC4775251 | biostudies-literature | 2015 Nov

REPOSITORIES: biostudies-literature

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

Garvin Tyler T   Aboukhalil Robert R   Kendall Jude J   Baslan Timour T   Atwal Gurinder S GS   Hicks James J   Wigler Michael M   Schatz Michael C MC  

Nature methods 20150907 11

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 cons  ...[more]

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