Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, Canada.
Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
Methods Mol Biol. 2023;2590:183-200. doi: 10.1007/978-1-0716-2819-5_12.
Dense local haplotypes can now readily be extracted from long-read or droplet-based sequence data. However, these methods struggle to combine subchromosomal haplotype blocks into global chromosome-length haplotypes. Strand-seq is a single cell sequencing technique that uses read orientation to capture sparse global phase information by sequencing only one of two DNA strands for each parental homolog. In combination with dense local haplotypes from other technologies, Strand-seq data can be used to obtain complete chromosome-length phase information. In this chapter, we run the R package StrandPhaseR to phase SNVs using publicly available sequence data for sample HG005 of the Genome in a Bottle project.
现在，可以轻松地从长读或液滴式测序数据中提取密集的局部单倍型。然而，这些方法在将亚染色体单倍型块组合成全局染色体长度单倍型方面存在困难。Strand-seq 是一种单细胞测序技术，它通过仅对每个亲本同源物的两条 DNA 链中的一条进行测序，利用读取方向来捕获稀疏的全局相位信息。与来自其他技术的密集局部单倍型结合使用，Strand-seq 数据可用于获得完整的染色体长度相位信息。在本章中，我们使用基因组瓶项目样本 HG005 的公开可用序列数据运行 R 包 StrandPhaseR 对 SNVs 进行相位分析。
