Goodman Simon J, Carr Ian M
School of Biology, Faculty of Biological Science, University of Leeds, Leeds, LS2 9JT, UK.
Leeds Institute of Medical Research at St James's, School of Medicine, University of Leeds, Leeds, LS9 7TF, UK.
Bioinformatics. 2024 Jul 13;40(7). doi: 10.1093/bioinformatics/btae450.
Mitochondrial DNA sequences are used extensively in phylogeographic and phylogenetic studies for a wide range of organisms. With the advent of low-cost, high throughput 'next generation' DNA sequencing, and user-friendly bioinformatics pipelines for generating and annotating whole mitochondrial genome assemblies, the analysis of whole mitochondrial genomes has become an important component of phylogenomic studies for taxa with high species diversity but limited coverage for other genomic resources. An important step in characterizing de novo mitochondrial genome assemblies is to evaluate and describe structural rearrangements relative to reference taxa. Accessible tools are needed to help visualize gene and noncoding feature complement, their order and strand orientation. However, there are few dedicated applications that generate high quality genome diagrams. Here we present circularMT and circularMT-console that allow users to create highly customizable, publication quality images, of linear and circular mitochondrial genome maps, either individually, or integrated into an analysis pipeline.
Both applications are implemented in C#, with binaries, source code and user guides available on GitHub (https://github.com/msjimc/circularMT). An archive of the published version is available on Zenodo (https://zenodo.org/records/10912319).
This paper has no supplementary data.
线粒体DNA序列在广泛的生物类群的系统地理学和系统发育研究中被广泛使用。随着低成本、高通量的“下一代”DNA测序技术的出现，以及用于生成和注释全线粒体基因组组装的用户友好型生物信息学管道的出现，对于物种多样性高但其他基因组资源覆盖有限的分类群，全线粒体基因组分析已成为系统基因组学研究的重要组成部分。表征从头线粒体基因组组装的一个重要步骤是评估和描述相对于参考分类群的结构重排。需要可访问的工具来帮助可视化基因和非编码特征互补、它们的顺序和链方向。然而，很少有专门的应用程序能够生成高质量的基因组图。在这里，我们展示了circularMT和circularMT-console，它们允许用户创建高度可定制的、具有出版物质量的线性和环形线粒体基因组图谱图像，可以单独创建，也可以集成到分析管道中。
这两个应用程序均用C#实现，二进制文件、源代码和用户指南可在GitHub（https://github.com/msjimc/circularMT）上获取。已发布版本的存档可在Zenodo（https://zenodo.org/records/10912319）上获取。
本文没有补充数据。
