Interactive analysis and assessment of single-cell copy-number variations
T Garvin, R Aboukhalil, J Kendall, T Baslan, GS Atwal… - Nature …, 2015 - nature.com
Nature methods, 2015•nature.com
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.
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.
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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