Roary

Roary constructs pan-genomes from annotated prokaryotic genome assemblies to identify core and accessory genes across isolates for comparative population analyses.

Key Features:

• Pan-genome construction: Calculates the pan-genome for prokaryotic populations from input genome annotations.
• Core and accessory gene identification: Identifies core genes shared among isolates and accessory genes that vary between them.
• Input format: Processes annotated assemblies in GFF3 format, typically generated using Prokka (Seemann, 2014).
• Scalability: Designed to handle large datasets comprising hundreds to thousands of isolates.
• Performance: Demonstrated to construct a pan-genome from 1,000 isolates in approximately 4.5 hours using 13 GB of RAM.
• Parallelization: Can leverage multiple processors to improve runtime.
• Implementation: Implemented in Perl.
• Accuracy and efficiency: Provides high accuracy in gene clustering while maintaining computational efficiency.

Scientific Applications:

• Comparative genomics: Analysis of gene presence–absence across prokaryotic isolates to define species- or population-level gene repertoires.
• Core/accessory genome characterization: Determination of conserved core genes and variable accessory genes for functional and evolutionary studies.
• Population genomics and evolutionary analysis: Investigation of genetic diversity and evolutionary dynamics within prokaryotic populations.

Methodology:

Processes annotated assemblies in GFF3 format (typically from Prokka) to calculate the pan-genome and identify core and accessory genes; implemented in Perl and supports multi-processor execution.