2025/12/29 by Lauren Coombe, Parham Kazemi, Johnathan Wong +2 · 1 voice · 10 citations
Biochemistry, Genetics and Molecular Biology · #Genome Rearrangement Algorithms #Genomics and Phylogenetic Studies #Fractal and DNA sequence analysis
paper · pdf · doi:10.1186/s12915-025-02455-w
BACKGROUND: With the growing availability of reference-grade genome assemblies across diverse taxa, there is an increasing need for efficient and scalable tools for multi-species comparative genomics, including synteny detection. Here, we introduce ntSynt, a scalable utility for computing large-scale multi-genome synteny using an alignment-free, minimizer graph-based approach. RESULTS: Through benchmarking on vertebrate genomes (~ 3 Gbp) and 11 bee genomes, we demonstrate that ntSynt produces accurate synteny maps with high genome coverage (79-100%) while using modest computational resources (~ 2 h, 34 GB memory). CONCLUSIONS: ntSynt's efficiency and scalability enable large-scale comparative analyses across the tree of life, providing a robust foundation for downstream comparative and functional genomic studies.