Vogel Ivan, Cai Lishan, Jerman-Plesec Lea, Hoffmann Eva R
DNRF Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
F1000Res. 2021 Sep 21;10:953. doi: 10.12688/f1000research.53287.1. eCollection 2021.
Genotyping of single cells using single nucleotide polymorphism arrays is a cost-effective technology that provides good coverage and precision, but requires whole genome amplification (WGA) due to the low amount of genetic material. Since WGA introduces noise, we recently developed SureTypeSC, an algorithm to minimize genotyping errors. Here, we present SureTypeSCR, an R package that integrates a state-of-the-art algorithm (SureTypeSC) for noise reduction in single cell genotyping and unites all common parts of genotyping workflow in a single tool. SureTypeSCR is built on top of the tidyverse ecosystem, which facilitates common operations over the data and allows users to create and experiment with the genotyping pipeline. Furthermore, the workflow of SureTypeSCR can also be used for standard genotyping of bulk DNA for batch processing in a single pipeline. SureTypeSCR is avaliable from: https://github.com/Meiomap/SureTypeSCR.
使用单核苷酸多态性阵列对单细胞进行基因分型是一种经济高效的技术，它能提供良好的覆盖范围和精度，但由于遗传物质数量少，需要进行全基因组扩增（WGA）。由于WGA会引入噪声，我们最近开发了SureTypeSC，一种将基因分型错误降至最低的算法。在这里，我们展示了SureTypeSCR，一个R包，它集成了一种用于单细胞基因分型中降噪的先进算法（SureTypeSC），并将基因分型工作流程的所有常见部分整合到一个工具中。SureTypeSCR基于tidyverse生态系统构建，这便于对数据进行常见操作，并允许用户创建和试验基因分型流程。此外，SureTypeSCR的工作流程也可用于批量DNA的标准基因分型，以便在单个流程中进行批量处理。SureTypeSCR可从以下网址获取：https://github.com/Meiomap/SureTypeSCR 。
