Perrin Amandine, Rocha Eduardo P C
Microbial Evolutionary Genomics, CNRS, UMR3525, Institut Pasteur, 28, rue Dr Roux, Paris 75015, France.
NAR Genom Bioinform. 2021 Jan 12;3(1):lqaa106. doi: 10.1093/nargab/lqaa106. eCollection 2021 Mar.
The study of the gene repertoires of microbial species, their pangenomes, has become a key part of microbial evolution and functional genomics. Yet, the increasing number of genomes available complicates the establishment of the basic building blocks of comparative genomics. Here, we present PanACoTA (https://github.com/gem-pasteur/PanACoTA), a tool that allows to download all genomes of a species, build a database with those passing quality and redundancy controls, uniformly annotate and then build their pangenome, several variants of core genomes, their alignments and a rapid but accurate phylogenetic tree. While many programs building pangenomes have become available in the last few years, we have focused on a modular method, that tackles all the key steps of the process, from download to phylogenetic inference. While all steps are integrated, they can also be run separately and multiple times to allow rapid and extensive exploration of the parameters of interest. PanACoTA is built in Python3, includes a singularity container and features to facilitate its future development. We believe PanACoTa is an interesting addition to the current set of comparative genomics tools, since it will accelerate and standardize the more routine parts of the work, allowing microbial genomicists to more quickly tackle their specific questions.
对微生物物种基因库（即它们的泛基因组）的研究已成为微生物进化和功能基因组学的关键部分。然而，可用基因组数量的不断增加使得比较基因组学基本构建单元的确定变得复杂。在此，我们展示了PanACoTA（https://github.com/gem - pasteur/PanACoTA），这是一种工具，它能够下载一个物种的所有基因组，利用通过质量和冗余控制的基因组构建数据库，进行统一注释，然后构建其泛基因组、核心基因组的多个变体、它们的比对以及一棵快速而准确的系统发育树。尽管在过去几年中出现了许多构建泛基因组的程序，但我们专注于一种模块化方法，该方法处理从下载到系统发育推断这一过程的所有关键步骤。虽然所有步骤都是集成的，但它们也可以单独运行多次，以便对感兴趣的参数进行快速而广泛的探索。PanACoTA是用Python3编写的，包含一个奇点容器以及便于其未来开发的功能。我们相信PanACoTa是当前比较基因组学工具集的一个有趣补充，因为它将加速并规范工作中更常规的部分，使微生物基因组学家能够更快地解决他们的特定问题。
