Roder, Thomas; Oberhänsli, Simone; Shani, Noam; Bruggmann, Rémy (2022). OpenGenomeBrowser: a versatile, dataset-independent and scalable web platform for genome data management and comparative genomics. BMC Genomics, 23(1), p. 855. BioMed Central 10.1186/s12864-022-09086-3
|
Text
s12864-022-09086-3.pdf - Published Version Available under License Creative Commons: Attribution (CC-BY). Download (4MB) | Preview |
BACKGROUND
As the amount of genomic data continues to grow, there is an increasing need for systematic ways to organize, explore, compare, analyze and share this data. Despite this, there is a lack of suitable platforms to meet this need.
RESULTS
OpenGenomeBrowser is a self-hostable, open-source platform to manage access to genomic data and drastically simplifying comparative genomics analyses. It enables users to interactively generate phylogenetic trees, compare gene loci, browse biochemical pathways, perform gene trait matching, create dot plots, execute BLAST searches, and access the data. It features a flexible user management system, and its modular folder structure enables the organization of genomic data and metadata, and to automate analyses. We tested OpenGenomeBrowser with bacterial, archaeal and yeast genomes. We provide a docker container to make installation and hosting simple. The source code, documentation, tutorials for OpenGenomeBrowser are available at opengenomebrowser.github.io and a demo server is freely accessible at opengenomebrowser.bioinformatics.unibe.ch .
CONCLUSIONS
To our knowledge, OpenGenomeBrowser is the first self-hostable, database-independent comparative genome browser. It drastically simplifies commonly used bioinformatics workflows and enables convenient as well as fast data exploration.
Item Type: |
Journal Article (Review Article) |
|---|---|
Division/Institute: |
08 Faculty of Science > Department of Biology > Bioinformatics and Computational Biology |
UniBE Contributor: |
Roder, Thomas, Oberhänsli, Simone, Bruggmann, Rémy |
ISSN: |
1471-2164 |
Publisher: |
BioMed Central |
Language: |
English |
Submitter: |
Pubmed Import |
Date Deposited: |
09 Jan 2023 15:10 |
Last Modified: |
15 Jan 2023 02:18 |
Publisher DOI: |
10.1186/s12864-022-09086-3 |
PubMed ID: |
36575383 |
Uncontrolled Keywords: |
Comparative genomics Genome browser Genome database Open-source Self-hosted |
BORIS DOI: |
10.48350/176571 |
URI: |
https://boris.unibe.ch/id/eprint/176571 |
Actions (login required)
 |
Edit item |