The development of DNA sequencing technologies makes it possible to obtain reads originated from both copies of a chromosome (two parental chromosomes, or haplotypes) of a single individual. Reconstruction of both haplotypes (i.e., haplotype phasing) plays a crucial role in genetic analysis and provides relationship information between genetic variation and disease susceptibility. With the emerging third-generation sequencing technologies, most existing approaches for haplotype phasing suffer from performance issues to handle long and error-prone reads. We develop a divide-and-conquer algorithm, DCHap, to phase haplotypes using third-generation reads. We benchmark DCHap against three state-of-the-art phasing tools on both PacBio SMRT data and ONT Nanopore data. The experimental results show that DCHap generates more accurate or comparable results (measured by the switch errors) while being scalable for higher coverage and longer reads. DCHap is a fast and accurate algorithm for haplotype phasing using third-generation sequencing data. As the third-generation sequencing platforms continue improving on their throughput and read lengths, accurate and scalable tools like DCHap are important to improve haplotype phasing from the advances of sequencing technologies. The source code is freely available at https://github.com/yanboANU/Haplotype-phasing.

中文翻译：

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DCHap：用于第三代序列的分而治之的单倍型定相算法

DNA 测序技术的发展使得获得来自单个个体的染色体的两个拷贝（两个亲本染色体或单倍型）的读数成为可能。两种单倍型的重建（即单倍型定相）在遗传分析中起着至关重要的作用，并提供了遗传变异和疾病易感性之间的关系信息。随着新兴的第三代测序技术的出现，大多数现有的单倍型定相方法都存在处理长且容易出错的读取的性能问题。我们开发了一种分而治之的算法 DCHap，以使用第三代读取来对单倍型进行定相。我们在 PacBio SMRT 数据和 ONT Nanopore 数据上将 DCHap 与三个最先进的定相工具进行了基准测试。实验结果表明，DCHap 生成更准确或可比较的结果（通过开关错误测量），同时可扩展以实现更高的覆盖率和更长的读取。DCHap 是一种使用第三代测序数据进行单倍型定相的快速且准确的算法。随着第三代测序平台的通量和读取长度不断提高，DCHap 等准确且可扩展的工具对于通过测序技术的进步改进单倍型定相非常重要。源代码可在以下位置免费获得 DCHap 等准确且可扩展的工具对于通过测序技术的进步改进单倍型定相非常重要。源代码可在以下位置免费获得 DCHap 等准确且可扩展的工具对于通过测序技术的进步改进单倍型定相非常重要。源代码可在以下位置免费获得https://github.com/yanboANU/Haplotype-phasing.