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

ABSTRACT: 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 employ

SUBMITTER: Tang S 

PROVIDER: S-EPMC12447420 | biostudies-literature | 2025 Sep

REPOSITORIES: biostudies-literature