dBBQs: dataBase of Bacterial Quality scores

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• Genome sequencing costs are decreasing, leading to an exponential increase in publicly available genomic data.
• A significant portion of publicly available bacterial genome sequences are incomplete drafts of varying quality.
• Assessing genome quality is crucial for reliable downstream analyses and tool development.

Purpose of the Study:

• To systematically evaluate the quality of publicly available bacterial genomes.
• To develop a centralized, user-friendly database for accessing bacterial genome quality scores.
• To provide a resource for identifying high-quality bacterial genomes for research purposes.

Main Methods:

• Collected and curated prokaryotic genomic data from major public repositories.
• Developed a genome quality scoring system based on assembly quality, gene content (rRNA, tRNA), and conserved functional domains.
• Implemented a database (dBBQs) for storing, searching, and retrieving genome quality scores.
• Visualized search results using an interactive JavaScript charting framework (DC.js).

Main Results:

• Calculated quality scores for approximately 100,000 bacterial genomes.
• Found that around 68% of analyzed bacterial genomes are of acceptable quality for many applications.
• Established the dataBase of Bacterial Quality scores (dBBQs) with fast search and download functionalities.
• Demonstrated the utility of dBBQs for filtering and selecting high-quality genomes.

Conclusions:

• The dBBQs database provides essential genome quality information for all available prokaryotic genome sequences.
• dBBQs facilitates the selection of high-quality genomes for testing bioinformatics tools and improving analytical accuracy.
• The database is regularly updated and freely accessible for non-commercial use, supporting the broader research community.