dBBQs

dBBQs calculates quality scores for bacterial genomes to quantify assembly quality, rRNA and tRNA gene content, and presence of conserved functional domains for comparative genomic selection and benchmarking.

Key Features:

• Genome collection: Calculates quality scores for approximately 100,000 bacterial genomes sourced from major public genome repositories.
• Non-redundant aggregation: Aggregates prokaryotic genomic data to create a non-redundant set of bacterial genomes.
• Assembly quality metric: Evaluates assembly quality as one of four distinct metrics used to score genomes.
• rRNA and tRNA gene metrics: Counts the number of ribosomal RNA (rRNA) and transfer RNA (tRNA) genes for each genome as separate metrics.
• Conserved functional domains metric: Assesses the presence of conserved functional domains as a metric of genomic completeness and annotation quality.
• Composite genome quality score: Combines the four metrics into an overall genome quality score and provides the underlying measurements for each genome.

Scientific Applications:

• Genome selection for benchmarking: Enables selection of high-quality bacterial genomes for testing bioinformatics tools and benchmarking analyses.
• Quality-threshold filtering: Supports setting quality score thresholds to select genomes suitable for downstream comparative genomics and method development.
• Repository quality assessment: Provides an empirical estimate that approximately 68% of bacterial genomes in major public databases meet predefined acceptable quality standards.

Methodology:

Aggregates prokaryotic genomic data into a non-redundant set, calculates four metrics for each genome—assembly quality, number of rRNA genes, number of tRNA genes, and presence of conserved functional domains—and combines those metrics into an overall genome quality score for ~100,000 bacterial genomes sourced from major repositories.