PMAT2: An efficient graphical assembly toolkit for comprehensive organellar genomes

作者：Fuchuan Han, Changwei Bi, Yicun Chen, Xiaogang Dai, Zefu Wang, Huaitong Wu, Ning Sun, Yanshu Qu, Yang Yang, Yangdong Wang, Tongming Yin · 发表于：iMeta · 年份：2025 · DOI：10.1002/imt2.70064 · 被引用次数：11 · 研究领域：RNA and protein synthesis mechanisms、Genomics and Phylogenetic Studies、Machine Learning in Bioinformatics

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.