HiMT: An integrative toolkit for assembling organelle genomes using HiFi reads

Chloroplast and mitochondrial genomes, which coexist with the nuclear genome, are extensively used in gene function studies, evolutionary analyses, and targeted breeding. However, assembling these organelle genomes remains challenging due to frequent recombination events and abundant repetitive sequences. Although some assembly tools are available, many are difficult to install or require extensive parameter tuning and computational resources. To address these limitations, we present a high-fidelity, data-driven mitochondrial genome assembly toolkit (HiMT), a user-friendly, out-of-the-box software solution that enables one-click chloroplast and mitochondrial genome assembly using default parameters, particularly for plant species. HiMT automatically estimates read coverage depth and employs a fixed k-mer prefix strategy to minimize computational demands, making it suitable for use on standard laptops. Benchmark tests show that HiMT delivers complete assemblies with a high success rate, fast runtimes, and low hardware requirements. Additionally, HiMT features a graphical user interface (GUI) and generates interactive reports for assessing the quality of organelle genome assemblies. We anticipate that HiMT will facilitate high-quality plant mitochondrial genome research and significantly streamline organelle genome assembly workflows. To support the research community, HiMT is freely available to non-commercial users at https://github.com/tang-shuyuan/HiMT.