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Chromonomer: A Tool Set for Repairing and Enhancing Assembled Genomes Through Integration of Genetic Maps and Conserved Synteny.
G3: Genes, Genomes, Genetics ( IF 2.6 ) Pub Date : 2020-10-27 , DOI: 10.1534/g3.120.401485
Julian Catchen 1 , Angel Amores 2 , Susan Bassham 3
Affiliation  

The pace of the sequencing and computational assembly of novel reference genomes is accelerating. Though DNA sequencing technologies and assembly software tools continue to improve, biological features of genomes such as repetitive sequence as well as molecular artifacts that often accompany sequencing library preparation can lead to fragmented or chimeric assemblies. If left uncorrected, defects like these trammel progress on understanding genome structure and function, or worse, positively mislead this research. Fortunately, integration of additional, independent streams of information, such as a marker-dense genetic map and conserved orthologous gene order from related taxa, can be used to scaffold together unlinked, disordered fragments and to restructure a reference genome where it is incorrectly joined. We present a tool set for automating these processes, one that additionally tracks any changes to the assembly and to the genetic map, and which allows the user to scrutinize these changes with the help of web-based, graphical visualizations. Chromonomer takes a user-defined reference genome, a map of genetic markers, and, optionally, conserved synteny information to construct an improved reference genome of chromosome models: a "chromonome". We demonstrate Chromonomer’s performance on genome assemblies and genetic maps that have disparate characteristics and levels of quality.



中文翻译:

色单体:通过整合遗传图谱和保守同义来修复和增强组装的基因组的工具集。

新参考基因组的测序和计算组装的步伐正在加快。尽管DNA测序技术和组装软件工具不断改进,但基因组的生物学特征(例如重复序列以及通常伴随测序文库制备的分子伪像)可能导致片段化或嵌合组装。如果不加以纠正,诸如这些践踏分子的缺陷会在理解基因组结构和功能上发展,或更糟的是,肯定会误导这项研究。幸运的是,可以使用其他独立信息流的整合,例如标记密集的遗传图谱和相关分类单元的保守直系同源基因顺序,来将未链接的,无序的片段支架在一起,并重组不正确连接的参考基因组。我们提供了一种用于自动化这些过程的工具集,该工具集还可以跟踪对装配和遗传图谱的任何更改,并允许用户借助基于Web的图形可视化检查这些更改。染色体单体采用用户定义的参考基因组,遗传标记图和可选的保守同义信息来构建染色体模型的改进参考基因组:“染色体组”。我们在具有不同特征和质量水平的基因组组装和遗传图谱上证明了色单体的性能。遗传标记图,以及可选地保守的同源信息,以构建染色体模型的改进参考基因组:“染色体组”。我们在具有不同特征和质量水平的基因组组装和遗传图谱上证明了色单体的性能。遗传标记图,以及可选地保守的同源信息,以构建染色体模型的改进参考基因组:“染色体组”。我们在具有不同特征和质量水平的基因组组装和遗传图谱上证明了色单体的性能。

更新日期:2020-11-06
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