Resolving genomes at haplotype level is crucial for understanding the evolutionary history of polyploid species and for designing advanced breeding strategies. Polyploid phasing still presents considerable challenges, especially in regions of collapsing haplotypes.We present WhatsHap polyphase , a novel two-stage approach that addresses these challenges by (i) clustering reads and (ii) threading the haplotypes through the clusters. Our method outperforms the state-of-the-art in terms of phasing quality. Using a real tetraploid potato dataset, we demonstrate how to assemble local genomic regions of interest at the haplotype level. Our algorithm is implemented as part of the widely used open source tool WhatsHap.

中文翻译：

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Haplotype threading：从长读长精确的多倍体定相

在单倍型水平解析基因组对于了解多倍体物种的进化历史和设计先进的育种策略至关重要。多倍体定相仍然存在相当大的挑战，特别是在折叠单倍型的区域。我们提出了 WhatsHap polyphase，这是一种新的两阶段方法，通过 (i) 聚类读取和 (ii) 将单倍型穿过簇来解决这些挑战。我们的方法在相位质量方面优于最先进的方法。使用真正的四倍体马铃薯数据集，我们展示了如何在单倍型水平组装感兴趣的局部基因组区域。我们的算法是作为广泛使用的开源工具 WhatsHap 的一部分实现的。