ArticleNAR genomics and bioinformatics2021
PanACoTA: a modular tool for massive microbial comparative genomics.
Article in NAR genomics and bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 74 papers.
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74 citing papers in PubMed.
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- Genome-wide analysis of extended-spectrum beta-lactamase-producingFrontiers in microbiology · 2026Article
- Structural basis for Lamassu-based antiviral immunity and its evolution from DNA repair machinery.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Characterization and comparative genome analysis of a new Tequintavirus isolated on Salmonella enterica serotype Tennessee.BMC research notes · 2025Article
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- Unlocking data in Klebsiella lysogens to predict capsular type-specificity of phage depolymerases.Nature communications · 2025Article
14 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors.
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Abstract
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.
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Registered trials
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