{"title":"PMAT2：一个高效的综合细胞体基因组图形组装工具包","authors":"Fuchuan Han, Changwei Bi, Yicun Chen, Xiaogang Dai, Zefu Wang, Huaitong Wu, Ning Sun, Yanshu Qu, Yang Yang, Yangdong Wang, Tongming Yin","doi":"10.1002/imt2.70064","DOIUrl":null,"url":null,"abstract":"<p>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.\n\n <figure>\n <div><picture>\n <source></source></picture><p></p>\n </div>\n </figure></p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"4 4","pages":""},"PeriodicalIF":23.7000,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.70064","citationCount":"0","resultStr":"{\"title\":\"PMAT2: An efficient graphical assembly toolkit for comprehensive organellar genomes\",\"authors\":\"Fuchuan Han, Changwei Bi, Yicun Chen, Xiaogang Dai, Zefu Wang, Huaitong Wu, Ning Sun, Yanshu Qu, Yang Yang, Yangdong Wang, Tongming Yin\",\"doi\":\"10.1002/imt2.70064\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p>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.\\n\\n <figure>\\n <div><picture>\\n <source></source></picture><p></p>\\n </div>\\n </figure></p>\",\"PeriodicalId\":73342,\"journal\":{\"name\":\"iMeta\",\"volume\":\"4 4\",\"pages\":\"\"},\"PeriodicalIF\":23.7000,\"publicationDate\":\"2025-07-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.70064\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"iMeta\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://onlinelibrary.wiley.com/doi/10.1002/imt2.70064\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"MICROBIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"iMeta","FirstCategoryId":"1085","ListUrlMain":"https://onlinelibrary.wiley.com/doi/10.1002/imt2.70064","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"MICROBIOLOGY","Score":null,"Total":0}
PMAT2: An efficient graphical assembly toolkit for comprehensive organellar genomes
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.
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