JASPER: A fast genome polishing tool that improves accuracy of genome assemblies.
JASPER: A fast genome polishing tool that improves accuracy of genome assemblies.
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DOI：
10.1371/journal.pcbi.1011032
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发表时间：
2023-03
影响因子：
4.3
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中科院分区：
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长读段测序技术的进步极大地提高了基因组组装的连续性和完整性。使用最新的基于纳米孔的测序仪，我们可以从单个流动池中生成足够的人类基因组组装数据。有了这些序列的长读段数据，我们现在可以常规地生产从头基因组组装，其中一半或更多的基因组包含在兆碱基规模的重叠群中。然而，仅从纳米孔数据产生的组件具有相对较高的错误率，并且可以从称为抛光的过程中受益，其中使用更准确的读数来纠正共有序列中的错误。在这篇手稿中，我们提出了一种新的基因组抛光工具，称为碧玉（基于水母的组装序列抛光器，用于减少错误）。与许多其他抛光方法相比，碧玉通过避免读取与组装的对齐来提高效率。相反，碧玉使用它从读段创建的k-mer计数数据库来检测和纠正共识中的错误。我们的实验表明，碧玉比基于k-mer的抛光方法更快，并且比其他基于k-mer的抛光方法更快和更准确。我们还介绍了使用抛光工具来创建群体特异性参考基因组的想法，并使用来自日本东京的多个个体的序列数据来说明这一想法。
Advances in long-read sequencing technologies have dramatically improved the contiguity and completeness of genome assemblies. Using the latest nanopore-based sequencers, we can generate enough data for the assembly of a human genome from a single flow cell. With the long-read data from these sequences, we can now routinely produce de novo genome assemblies in which half or more of a genome is contained in megabase-scale contigs. Assemblies produced from nanopore data alone, though, have relatively high error rates and can benefit from a process called polishing, in which more-accurate reads are used to correct errors in the consensus sequence. In this manuscript, we present a novel tool for genome polishing called JASPER (Jellyfish-based Assembly Sequence Polisher for Error Reduction). In contrast to many other polishing methods, JASPER gains efficiency by avoiding the alignment of reads to the assembly. Instead, JASPER uses a database of k-mer counts that it creates from the reads to detect and correct errors in the consensus. Our experiments demonstrate that JASPER is faster than alignment-based polishers, and both faster and more accurate than other k-mer based polishing methods. We also introduce the idea of using a polishing tool to create population-specific reference genomes, and illustrate this idea using sequence data from multiple individuals from Tokyo, Japan.