ArticleBMC biology2025
ntSynt: multi-genome synteny detection using minimizer graph mappings.
Article in BMC biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- A Mid-Atlantic Brook Trout (Salvelinus fontinalis) genome to advance conservation and comparative genomics.G3 (Bethesda, Md.) · 2026Article
- Four haplotype-resolved genome assemblies and a reference-free 66-haplotype pangenome graph for Cannabis sativa.Scientific data · 2026Article
- Navigating the pangenome coordinate system with Shredtools.bioRxiv : the preprint server for biology · 2026Article
- de novo Assembly of five Highly Contiguous Heliconius Butterfly Genomes With Long-Read Sequencing Alone.Genome biology and evolution · 2026Article
- Seqwin: ultrafast identification of signature sequences in microbial genomes.Bioinformatics (Oxford, England) · 2026Article
- Two Australian genome assemblies expand the genomic blueprint of giant kelp.BMC genomics · 2026Article
- A high-quality reference genome for the ornate shrew (Sorex ornatus).The Journal of heredity · 2026Article
- Genome assemblies of two bumble bee species: Bombus sonorus and Bombus vosnesenskii.The Journal of heredity · 2026Article
- Phage toxin variants are linked to protection specificity in a defensive symbiont.Molecular biology and evolution · 2026Article
- Haplotype-resolved genome assemblies of BJ and IMR-90 human fibroblast cell lines reveal extensive structural variation and enable reanalysis of historical sequencing data.Nucleic acids research · 2026Article
- Genome assembly and annotation of the olive grass mouse Abrothrix olivacea reveal transcriptomic and cellular adaptations across contrasting biomes.BMC genomics · 2026Article
- Recombination landscape shaped by inversion polymorphisms: a high-density linkage map and chromosome-level assembly of inversion-rich spruce bark beetle genome.G3 (Bethesda, Md.) · 2026Article
- Genomic erosion across avian lineages in the context of their evolutionary history.Molecular biology and evolution · 2026Article
- Chromosome-level genome assembly of the common tenrec, Tenrec ecaudatus (Schreber, 1778), a new model for early placental mammal evolution.BMC genomics · 2026Article
- A highly contiguous genome assembly for the California vole, Microtus californicus, provides insight into phylogenetic relationships and patterns of synteny among voles.The Journal of heredity · 2026Article
- First genome and transcription factor profile for Asimina triloba, a native North American fruit tree.The plant genome · 2026Article
- The potato cyst nematode Globodera pallida overcomes major potato resistance through selection on standing variation at a single locus.The New phytologist · 2026Article
- MoGAAAP: a modular Snakemake workflow for automated genome assembly and annotation with quality assessment.NAR genomics and bioinformatics · 2026Article
- A trio-binning approach for genome assembly reveals extensive structural variation between two Cannabis cultivars: Punto Rojo and Cherry Pie.G3 (Bethesda, Md.) · 2026Article
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Authors and funding
5 authors.
Funding
Abstract
backgroundWith 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.
resultsThrough 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).
conclusionsntSynt'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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.