Oatk: a de novo assembly tool for complex plant organelle genomes
Chenxi Zhou, Max R. Brown, Mark Blaxter, Shane McCarthy, Richard Durbin
Abstract
Plant organelle genomes, particularly large mitochondrial genomes with complex repeats, present significant challenges for assembly. The advent of long-read sequencing enables the assembly of complete genomes, but problems of resolving alternative structures remain. Here we introduce a novel tool that employs a syncmer-based assembler for rapid assembly graph construction, integrates a profile-HMM database for robust organelle identification, and leverages a new search method to find the best supported path through the assembly graph. We describe high-quality organelle assemblies for 195 plant species, demonstrating improvements over other methods, and providing multiple insights into structural complexity, heteroplasmy, and DNA exchange between organelles.