GenomeDepot Enables Web-Based Annotation and Comparative Analysis of Microbial Genomes
GenomeDepot is an open-source, web-based platform for microbial genome annotation, management, and comparative analysis. Built to help researchers quickly organize genome collections and explore genomic features, including ortholog families, protein domains, operons, regulatory interactions, and strain and sample metadata, GenomeDepot also enables interactive genome browsing, BLAST and annotation search, and comparative genomic neighborhood visualization, with easy sequence download. A customizable annotation pipeline runs tools in Conda environments and can be extended with additional analyses. GenomeDepot is available under the GNU General Public License on GitHub (https://github.com/aekazakov/genome- depot), with installation documentation at https://aekazakov.github.io/genome-depot/ and a public demo server at https://iseq.lbl.gov/demogd/.
Overview of GenomeDepot key capabilities:
Impact to Field/Science
With GenomeDepot, research teams can organize their genome collections, combine them with genomes downloaded from public sources, run an array of annotation tools, and present them in web-portals.
Significance to ENIGMA
We used GenomeDepot for the creation of three online genome collections. The first is a publicly accessible dataset of 2205 bacterial and archaeal genomes, including 339 published ENIGMA genomes (https://iseq.lbl.gov/genomes/). The second is an internal ENIGMA genome collection of 3105 genomes including 2318 ENIGMA published, unpublished and draft genomes (https://iseq.lbl.gov/genomes-enigma/). Finally, a collection of 262 isolate genomes and metagenome-assembled genomes of Rhodanobacter, a taxon of special interest for ENIGMA (https://iseq.lbl.gov/rhodano/).
Publication
Alexey Kazakov, Adam M Deutschbauer, GenomeDepot: data management system for microbial comparative genomics, Bioinformatics Advances, Volume 6, Issue 1, 2026, vbag027, [DOI]:10.1093/bioadv/vbag027. OSTI:3020594