Comparative evaluation of Nanopore polishing tools for microbial genome assembly and polishing strategies for downstream analysis.
Comparative evaluation of Nanopore polishing tools for microbial genome assembly and polishing strategies for downstream analysis.
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DOI：
10.1038/s41598-021-00178-w
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发表时间：
2021-10-20
影响因子：
4.6
通讯作者：
Kwak W
中科院分区：
文献类型：
--
作者：
Lee JY;Kong M;Oh J;Lim J;Chung SH;Kim JM;Kim JS;Kim KH;Yoo JC;Kwak W
仅使用Flongle等经济高效的Nanopore长读长系统组装高质量的微生物基因组对于加速微生物基因组的研究非常重要，而其中最关键的一点是抛光过程。在这项研究中，我们根据 BUSCO 和 Prokka 基因预测，对八种最先进的 Nanopore 抛光工具和可用组合的微生物基因组组装进行了评估。在单个工具的评估中，Homopolish、PEPPER 和 Medaka 表现出了比其他工具更好的结果。在组合抛光方面，第二轮Homopolish和PEPPER×青鳉组合也表现出了比其他组合更好的效果。然而，单个工具和组合在使用和结果方面有特定的限制。根据目标生物体和下游研究的目的，已证实通过添加短读来完美替代混合抛光仍然存在一些困难。尽管如此，通过不断改进蛋白质孔、相关碱基识别算法以及基于改进的错误模型的抛光工具，仅使用纳米孔读长即可获得高质量的微生物基因组，而无需产生额外的短读长数据。本研究提出的精加工策略预计将为仅使用纳米孔读数组装微生物基因组提供有用的信息，具体取决于目标微生物和研究目的。
Assembling high-quality microbial genomes using only cost-effective Nanopore long-read systems such as Flongle is important to accelerate research on the microbial genome and the most critical point for this is the polishing process. In this study, we performed an evaluation based on BUSCO and Prokka gene prediction in terms of microbial genome assembly for eight state-of-the-art Nanopore polishing tools and combinations available. In the evaluation of individual tools, Homopolish, PEPPER, and Medaka demonstrated better results than others. In combination polishing, the second round Homopolish, and the PEPPER × medaka combination also showed better results than others. However, individual tools and combinations have specific limitations on usage and results. Depending on the target organism and the purpose of the downstream research, it is confirmed that there remain some difficulties in perfectly replacing the hybrid polishing carried out by the addition of a short-read. Nevertheless, through continuous improvement of the protein pores, related base-calling algorithms, and polishing tools based on improved error models, a high-quality microbial genome can be achieved using only Nanopore reads without the production of additional short-read data. The polishing strategy proposed in this study is expected to provide useful information for assembling the microbial genome using only Nanopore reads depending on the target microorganism and the purpose of the research.
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影响因子：
3.7
作者：
Walker BJ;Abeel T;Shea T;Priest M;Abouelliel A;Sakthikumar S;Cuomo CA;Zeng Q;Wortman J;Young SK;Earl AM
通讯作者：
Earl AM
影响因子：
5.8
作者：
Firtina, Can;Kim, Jeremie S.;Mutlu, Onur
通讯作者：
Mutlu, Onur
影响因子：
9.5
作者：
Thorvaldsdóttir H;Robinson JT;Mesirov JP
通讯作者：
Mesirov JP
影响因子：
12.3
作者：
Huang YT;Liu PY;Shih PW
通讯作者：
Shih PW
影响因子：
5.8
作者：
Li, Heng
通讯作者：
Li, Heng