Abstract
GenomeDepot is a 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 web-sites for user-defined genome collections that include bioinformatic tools for interactive genome browsing, 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.
- Developers:
-
Kazakov, Alexey [1]
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Release Date:
- 2025-08-28
- Project Type:
- Open Source, Publicly Available Repository
- Software Type:
- Scientific
- Licenses:
-
GNU General Public License v3.0
- Sponsoring Org.:
-
USDOEPrimary Award/Contract Number:AC02-05CH11231
- Code ID:
- 162195
- Site Accession Number:
- 2025-194
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Country of Origin:
- United States
Citation Formats
Kazakov, Alexey.
GenomeDepot v1.0.
Computer Software.
https://github.com/aekazakov/genome-depot.
USDOE.
28 Aug. 2025.
Web.
doi:10.11578/dc.20250829.11.
Kazakov, Alexey.
(2025, August 28).
GenomeDepot v1.0.
[Computer software].
https://github.com/aekazakov/genome-depot.
https://doi.org/10.11578/dc.20250829.11.
Kazakov, Alexey.
"GenomeDepot v1.0." Computer software.
August 28, 2025.
https://github.com/aekazakov/genome-depot.
https://doi.org/10.11578/dc.20250829.11.
@misc{
doecode_162195,
title = {GenomeDepot v1.0},
author = {Kazakov, Alexey},
abstractNote = {GenomeDepot is a 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 web-sites for user-defined genome collections that include bioinformatic tools for interactive genome browsing, 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.},
doi = {10.11578/dc.20250829.11},
url = {https://doi.org/10.11578/dc.20250829.11},
howpublished = {[Computer Software] \url{https://doi.org/10.11578/dc.20250829.11}},
year = {2025},
month = {aug}
}