RT Journal Article
SR Electronic
T1 PanACoTA: A modular tool for massive microbial comparative genomics
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.09.11.293472
DO 10.1101/2020.09.11.293472
A1 Amandine Perrin
A1 Eduardo P.C. Rocha
YR 2020
UL http://biorxiv.org/content/early/2020/09/18/2020.09.11.293472.abstract
AB The study of the gene repertoires of microbial species, their pangenomes, has become a key topic of study in microbial evolution and 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. The software is built in Python3 and includes 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.Competing Interest StatementThe authors have declared no competing interest.