cogeqc

cogeqc facilitates systematic quality checks on standard comparative genomics analyses to help researchers detect issues and select the most suitable parameters for each data set.

Key Features:

• Genome Assembly and Annotation Quality Assessment: Evaluates genome assembly and annotation quality using BUSCOs and compares statistics with publicly available genomes on NCBI.
• Orthogroup Inference Assessment: Calculates a protein domain-aware orthogroup score that maximises the number of shared protein domains within the same orthogroup.
• Synteny Detection Assessment: Represents anchor gene pairs as a synteny network and analyses graph properties including clustering coefficient, node count, and scale-free topology fit.
• Data Visualization: Provides functions to explore QC summary statistics.

Scientific Applications:

• Comparative Genomics Quality Control: Enables context-guided assessments of assembly and annotation statistics by comparing observed statistics to those of closely-related species on NCBI.
• Parameter Optimization for Orthogroup Inference: Allows evaluation of multiple parameter combinations for orthogroup identification tools to select the most appropriate parameters for specific data sets.
• Parameter Optimization for Synteny Detection: Allows evaluation of multiple parameter combinations for synteny detection tools to select the most appropriate parameters for specific data sets.

Methodology:

The package uses BUSCO analysis, NCBI genome statistics comparisons, protein domain-based orthogroup scoring, and synteny network graph property analysis including clustering coefficient, node count, and scale-free topology fit.