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Background <p>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.</p> Results <p>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&#xa0;h, 34&#xa0;GB memory).</p> Conclusions <p>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.</p>

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ntSynt: multi-genome synteny detection using minimizer graph mappings

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年12月29日

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  • Lauren Coombe,
  • Parham Kazemi,
  • Johnathan Wong,
  • Inanc Birol,
  • René L. Warren

摘要

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.