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MOMS: A pipeline for scaffolding using multi-optical maps

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资源类型：
WOS体系：
Pubmed体系：

收录情况： ◇ SCIE

作者：
Xu Jiang[1] * ; Liao Baosheng[1,2] * ; Guo Shuai[1] * ; Xiao Shuiming[1] * ; Liao Xuejiao[1,3] ; Jiang Hongshan[1] ; Zang Chen[1] ; Shen Xiaofeng[1] ; Chu Yang[1] ; Wu Wenguang[1,4] ; Dou Deqiang[5] ; Luo Lu[1] ; Li Qiushi[1] ; Yang Tae-Jin[6] ; Guo Yiming[7] ; Huang Zhihai[2] ; Chen Shilin[1,8] ;
机构： [1]Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China. [2]Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China. [3]Pharmacy College, Shandong University of Traditional Chinese Medicine, Jinan, China. [4]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]Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, China.
出处：
DOI： 10.1111/1755-0998.13842
ISSN：

关键词： directed node graph genome assembly minimum spanning tree optical mapping telomere-to-telomere assembly

摘要：
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.© 2023 John Wiley & Sons Ltd.

基金：
Fundamental Research Funds for the Central Public Welfare Research Institutes, Grant/Award Number: ZZ13-YQ- 047; National Natural Science Foundation of China, Grant/Award Number: 81891013 and U1812403-1; National Science and Technology Major Project, Grant/Award Number: 2017ZX09301060; National Science Foundation of China, Grant/Award Number: 82204610; National Key Research and Development Program of China, Grant/Award Number: 2017YFC702100
语种：
外文
WOS：
PubmedID：
中科院(CAS)分区：
出版当年[2022]版：
大类 | 1 区 生物学
小类 | 1 区 生化与分子生物学 2 区 生态学 2 区 进化生物学
最新[2025]版：
大类 | 1 区 生物学
小类 | 2 区 生化与分子生物学 2 区 生态学 2 区 进化生物学
JCR分区：
出版当年[2021]版：
Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Q1 ECOLOGY Q1 EVOLUTIONARY BIOLOGY
最新[2023]版：
Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Q1 ECOLOGY Q1 EVOLUTIONARY BIOLOGY

影响因子： 最新[2023版] 最新五年平均 出版当年[2021版] 出版当年五年平均 出版前一年[2020版] 出版后一年[2022版]

第一作者：
第一作者机构： [1]Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
共同第一作者：
通讯作者：
通讯机构： [1]Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China. [8]Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, China.
推荐引用方式(GB/T 7714)：
Xu Jiang,Liao Baosheng,Guo Shuai,et al.MOMS: A pipeline for scaffolding using multi-optical maps[J].MOLECULAR ECOLOGY RESOURCES.2023,23(8):1914-1929.doi:10.1111/1755-0998.13842.
APA：
Xu Jiang,Liao Baosheng,Guo Shuai,Xiao Shuiming,Liao Xuejiao...&Chen Shilin.(2023).MOMS: A pipeline for scaffolding using multi-optical maps.MOLECULAR ECOLOGY RESOURCES,23,(8)
MLA：
Xu Jiang,et al."MOMS: A pipeline for scaffolding using multi-optical maps".MOLECULAR ECOLOGY RESOURCES 23..8(2023):1914-1929

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