Garvin, T., Aboukhalil, R., Kendall, J., Baslan, T., Atwal, G. S., Hicks, J., Wigler, M., Schatz, M. C. (November 2015) Interactive analysis and assessment of single-cell copy-number variations. Nat Methods, 12. pp. 1058-1060. ISSN 1548-7105 (Electronic)1548-7091 (Linking) (Public Dataset)
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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.
| Item Type: | Paper |
|---|---|
| Subjects: | bioinformatics bioinformatics > computational biology bioinformatics > genomics and proteomics > computers > computer software bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > copy number variants |
| CSHL Authors: | |
| Communities: | CSHL Cancer Center Program > Cancer Genetics CSHL Cancer Center Program > Cancer Genetics and Genomics Program CSHL labs > Atwal lab CSHL labs > Hicks lab CSHL labs > Schatz lab CSHL labs > Wigler lab School of Biological Sciences > Publications |
| Depositing User: | Matt Covey |
| Date: | November 2015 |
| Date Deposited: | 11 Sep 2015 14:43 |
| Last Modified: | 15 Jul 2021 19:07 |
| PMCID: | PMC4775251 |
| Related URLs: | |
| Dataset ID: | |
| URI: | https://repository.cshl.edu/id/eprint/31762 |
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