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SCCNV: a software tool for identifying copy number variation from single-cell whole-genome sequencing

By Xiao Dong, Lei Zhang, Xiaoxiao Hao, Tao Wang, Jan Vijg

Posted 31 Jan 2019
bioRxiv DOI: 10.1101/535807 (published DOI: 10.3389/fgene.2020.505441)

Background: Identification of de novo mutations from cell populations requires single-cell whole-genome sequencing (SCWGS). Although many experimental protocols of SCWGS have been developed, few computational tools are available for downstream analysis of different types of somatic mutations, including copy number variation (CNV). Results: We developed SCCNV, a software tool for detecting CNVs from whole genome-amplified single cells. SCCNV is a read-depth based approach with adjustment for the whole-genome amplification bias. Conclusions: We demonstrate its performance by analyzing data collected from most of the single-cell amplification methods, including DOP-PCR, MDA, MALBAC and LIANTI. SCCNV is freely available at https://github.com/biosinodx/SCCNV.

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