B-B.04: zDB: bacterial comparative genomics made easy
The analysis and comparison of genomes can be complex, as it requires integrating and visualizing the results from various tools specialized for tasks such as orthology inference, phylogenetic inference, and structural and functional annotation. To simplify this process, we have developed zDB, an easy-to-use comparative genomics software integrating an analysis pipeline and a graphical user interface (GUI).
Starting from annotated Genbank files, zDB identifies orthologs and infers a phylogeny for each orthogroup as well as a species phylogeny constructed from shared single-copy orthologs. Pfam, COG, KEGG, antimicrobial resistance and virulence factor annotations can also be added to the genes, while homologs can be identified in the Swissprot and RefSeq databases. Finally, genomic islands can be predicted and their conservation evaluated across genomes.
This wealth of information can then be analysed in the GUI, which allows to search for specific genes or annotations, to perform BLAST queries, to compare genomic regions or whole genomes, to display the presence/absence of orthologs and annotations in subsets of genomes in various ways (heatmaps, presence/absence tables, Venn diagrams, phylogenies, etc.), and to compare metabolic capacities between genomes.
zDB is open-source (https://github.com/metagenlab/zDB), easy to install with conda and provides a command-line interface allowing to easily download the necessary reference databases, run the analysis pipeline and start the GUI. Overall zDB is easy to use while offering a wide range of features, making it useful both for bioinformaticians and researchers more accustomed to laboratory research. A demo of the GUI is available at https://zdb.metagenlab.ch/.
Co-authors: Bastian Marquis, Alessia Carrara, Trestan Pillonel, Claire Bertelli
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