GenomeDepot: data management system for microbial comparative genomics

TL;DR

GenomeDepot is a web-based platform for managing and analyzing microbial genomes, enabling interactive tools for annotation and comparative genomics.

Contribution

The novelty lies in providing a customizable and extensible platform for microbial genome analysis with integrated annotation pipelines and interactive tools.

Findings

GenomeDepot supports rapid creation of websites for genome collections with bioinformatic tools.

The platform includes a customizable annotation pipeline running in Conda environments.

A demo server and full documentation are publicly accessible for easy adoption.

Abstract

GenomeDepot is an open-source web-based platform for annotation, management, and comparative analysis of microbial genomic sequences and associated data including ortholog families, protein domains, operons, regulatory interactions, strain taxonomy, and sample metadata. GenomeDepot supports rapid creation of websites for user-defined genome collections that include bioinformatic tools for interactive genome browsing, Basic Local Alignment Search Tool (BLAST) search, annotation search, comparative genomic neighborhood visualization, and sequence download. Gene function annotations are generated by a customizable annotation pipeline. The pipeline runs annotation tools in Conda environments and can be easily extended with additional user-specified tools.

GenomeDepot is open source and distributed under the GNU General Public License via GitHub (https://github.com/aekazakov/genome-depot). GenomeDepot is implemented in Python and was tested in Ubuntu Linux. Full installation instructions and documentation are available at https://aekazakov.github.io/genome-depot/. GenomeDepot demo server is freely accessible at https://iseq.lbl.gov/demogd/.

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