Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Schwabenheimer Str. 101, 69221 Dossenheim, Germany.
Microb Genom. 2024 Jan;10(1). doi: 10.1099/mgen.0.001173.
Generating complete, high-quality genome assemblies is key for any downstream analysis, such as comparative genomics. For bacterial genome assembly, various algorithms and fully automated pipelines exist, which are free-of-charge and easily accessible. However, these assembly tools often cannot unambiguously resolve a bacterial genome, for example due to the presence of sequence repeat structures on the chromosome or on plasmids. Then, a more sophisticated approach and/or manual curation is needed. Such modifications can be challenging, especially for non-bioinformaticians, because they are generally not considered as a straightforward process. In this study, we propose a standardized approach for manual genome completion focusing on the popular hybrid assembly pipeline Unicycler. The provided Galaxy workflow addresses two weaknesses in Unicycler's hybrid assemblies: (i) collapse of inter-plasmidic repeats and (ii) false loss of single-copy sequences. To demonstrate and validate how to detect and resolve these assembly errors, we use two genomes from the group. By applying the proposed pipeline following an automated assembly, the genome sequence quality can be significantly improved.
生成完整、高质量的基因组组装对于任何下游分析（如比较基因组学）都是关键。对于细菌基因组组装，存在各种算法和全自动化的管道，它们是免费的，并且易于访问。然而，这些组装工具往往无法明确解析细菌基因组，例如由于染色体或质粒上存在序列重复结构。然后，需要更复杂的方法和/或手动编辑。这种修改可能具有挑战性，特别是对于非生物信息学家而言，因为它们通常不被认为是一个简单的过程。在这项研究中，我们针对流行的混合组装管道 Unicycler 提出了一种标准化的手动基因组完成方法。提供的 Galaxy 工作流程解决了 Unicycler 混合组装中的两个弱点：（i）质粒间重复结构的折叠和（ii）单拷贝序列的错误丢失。为了演示和验证如何检测和解决这些组装错误，我们使用了来自 组的两个基因组。通过在自动化组装后应用提出的管道，可以显著提高基因组序列质量。
