In this paper, we report a pipeline, AsmMix, which is capable of producing both contiguous and high-quality diploid genomes. The pipeline consists of two steps. In the first step, two sets of assemblies are generated: one is based on co-barcoded reads, which are highly accurate and haplotype-resolved but contain many gaps, the other assembly is based on single-molecule sequencing reads, which is contiguous but error-prone. In the second step, those two sets of assemblies are compared and integrated into a haplotype-resolved assembly with fewer errors. We test our pipeline using a dataset of human genome NA24385, perform variant calling from those assemblies and then compare against GIAB Benchmark. We show that AsmMix pipeline could produce highly contiguous, accurate, and haplotype-resolved assemblies. Especially the assembly mixing process could effectively reduce small-scale errors in the long read assembly.

中文翻译：

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AsmMix：高质量的二倍体从头组装流水线

在本文中，我们报告了一个名为AsmMix的管道，该管道能够产生连续和高质量的二倍体基因组。管道包括两个步骤。第一步，将生成两套程序集：一套基于高度精确且具有单倍型解析但有许多空位的共条形码读取，另一套则基于单分子测序读取，这是连续的，但容易出错。在第二步中，将这两组程序集进行比较，并以更少的错误将其集成到单倍型解析的程序集中。我们使用人类基因组NA24385的数据集测试管道，从这些程序集中执行变体调用，然后与GIAB Benchmark进行比较。我们证明了AsmMix管道可以产生高度连续，准确和单倍型解析的程序集。