PMAT2: An efficient graphical assembly toolkit for comprehensive organellar genomes

This is the authors' abstract. We don't add key points for this paper.

We developed PMAT2, an advanced toolkit for lineage-specific de novo assembly of plant, animal, and fungal mitochondrial genomes, as well as plant chloroplast genome. PMAT2 leverages optimized graph-based strategies tailored to organelle genome complexity, enabling complete and accurate assemblies, even with approximately 1 × highly accurate PacBio high-fidelity (HiFi) reads. By assembling 150 organellar genomes across diverse lineages, PMAT2 outperformed existing tools in assembly completeness. The source code for PMAT2 is publicly available at https://github.com/aiPGAB/PMAT2.