CoreDetector: a flexible and efficient program for core-genome alignment of evolutionary diverse genomes

Area of Science:

• Genomics
• Bioinformatics
• Comparative Genomics

Background:

• Whole genome alignment is crucial for identifying sequence variations and core genomes in eukaryotes.
• Existing tools struggle with large eukaryotic genomes and divergent species due to computational demands.
• There is a need for efficient and flexible tools for eukaryotic core-genome analysis.

Purpose of the Study:

• To introduce CoreDetector, a user-friendly program for aligning core-genome sequences across various genome sizes and divergence levels.
• To demonstrate the versatility of CoreDetector using fungal, wheat, fly, and rodent genomes.
• To compare CoreDetector's performance against existing multiple genome alignment tools.

Main Methods:

• CoreDetector was developed in Java for cross-platform compatibility and easy deployment.
• A packaged pipeline is executable via bash terminal, requiring no external environments.
• The tool was tested on diverse datasets, including fungal pathogens, wheat cultivars, and rodent/fly species.

Main Results:

• CoreDetector successfully aligned core-genome sequences for a range of genome sizes and divergence levels.
• Alignments of fungal, wheat, fly, and rodent genomes demonstrated CoreDetector's flexibility.
• CoreDetector showed improved flexibility, efficiency, and competitive accuracy compared to existing tools.

Conclusions:

• CoreDetector offers an effective solution for eukaryotic core-genome alignment.
• The tool's ease of use and performance make it valuable for genomic research.
• CoreDetector provides a flexible and efficient alternative for analyzing sequence and structural variations.