Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies
Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies
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DOI：
10.1186/s13059-020-02134-9
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发表时间：
2020-09-14
期刊：
影响因子：
12.3
通讯作者：
Phillippy, Adam M.
中科院分区：
文献类型：
--
作者：
Rhie, Arang;Walenz, Brian P.;Phillippy, Adam M.
最近的长时间阅读组装常常超过可用的参考基因组的质量和完整性，使得验证具有挑战性。在这里，我们介绍了Merqury，一个新的基于高效k-mer集合运算的无引用汇编评估工具。通过将从头组装的k-MERS与未组装的高精度读数中的k-MERS进行比较，Merqury估计了基本水平的准确性和完整性。对于TRIO，Merqury还可以评估特定于单倍型的准确性、完整性、相块连续性和开关误差。可以生成用于评估的多种可视化，例如k-mer谱图。我们在人类和植物基因组上都证明了Merqury是一种快速和健壮的组装验证方法。
Recent long-read assemblies often exceed the quality and completeness of available reference genomes, making validation challenging. Here we present Merqury, a novel tool for reference-free assembly evaluation based on efficient k-mer set operations. By comparing k-mers in a de novo assembly to those found in unassembled high-accuracy reads, Merqury estimates base-level accuracy and completeness. For trios, Merqury can also evaluate haplotype-specific accuracy, completeness, phase block continuity, and switch errors. Multiple visualizations, such as k-mer spectrum plots, can be generated for evaluation. We demonstrate on both human and plant genomes that Merqury is a fast and robust method for assembly validation.