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MOMS: A pipeline for scaffolding using multi-optical maps |
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| Authors: | Jiang Xu Baosheng Liao Shuai Guo Shuiming Xiao Xuejiao Liao Hongshan Jiang Chen Zang Xiaofeng Shen Yang Chu Wenguang Wu Deqiang Dou Lu Luo Qiushi Li Tae-Jin Yang Yiming Guo Zhihai Huang Shilin Chen |
| Institution: | 1. Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China;2. Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China;3. Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China Pharmacy College, Shandong University of Traditional Chinese Medicine, Jinan, China;4. Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China Artemisinin Research Center, China Academy of Chinese Medical Sciences, Beijing, China;5. College of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China;6. Department of Plant Science, Seoul National University, Seoul, South Korea;7. Kenneth P. Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA;8. Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China |
| Abstract: | Here, we report a new multi-optical maps scaffolder (MOMS) aiming at utilizing complementary information among optical maps labelled by distinct enzymes. This pipeline was designed for data structure organization, scaffolding by path traversal, gap-filling and molecule reuse of optical maps. Our testing showed that this pipeline has uncapped enzyme tolerance in scaffolding. This means that there are no inbuilt limits as to the number of maps generated by different enzymes that can be utilized by MOMS. For the genome assembly of the human GM12878 cell line, MOMS significantly improved the contiguity and completeness with an up to 144-fold increase of scaffold N50 compared with initial assemblies. Benchmarking on the genomes of human and O. sativa showed that MOMS is more effective and robust compared with other optical-map-based scaffolders. We believe this pipeline will contribute to high-fidelity chromosome assembly and chromosome-level evolutionary analysis. |
| Keywords: | directed node graph genome assembly minimum spanning tree optical mapping telomere-to-telomere assembly |