MOMS: A pipeline for scaffolding using multi-optical maps

被引：0

作者：

Xu, Jiang ^{[1
,9
]}

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
,9
]}

机构：

[1] China Acad Chinese Med Sci, Inst Chinese Mat Med, Beijing, Peoples R China

[2] Guangzhou Univ Chinese Med, Guangdong Prov Hosp Chinese Med, Affiliated Hosp 2, Guangzhou, Peoples R China

[3] Shandong Univ Tradit Chinese Med, Pharm Coll, Jinan, Peoples R China

[4] China Acad Chinese Med Sci, Artemisinin Res Ctr, Beijing, Peoples R China

[5] Liaoning Univ Tradit Chinese Med, Coll Pharm, Dalian, Peoples R China

[6] Seoul Natl Univ, Dept Plant Sci, Seoul, South Korea

[7] Univ Pittsburgh, Kenneth P Dietrich Sch Arts & Sci, Pittsburgh, PA USA

[8] Chengdu Univ Tradit Chinese Med, Pharm Coll, Chengdu, Peoples R China

[9] China Acad Chinese Med Sci, Inst Chinese Mat Med, Beijing 100700, Peoples R China

来源：

MOLECULAR ECOLOGY RESOURCES | 2023年 / 23卷 / 08期

基金：

中国国家自然科学基金; 美国国家科学基金会;

关键词：

directed node graph; genome assembly; minimum spanning tree; optical mapping; telomere-to-telomere assembly; GENOME ASSEMBLIES; PAIRED-END; ALIGNMENT; TOOL;

D O I：

10.1111/1755-0998.13842

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

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.

引用

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页码：1914 / 1929

页数：16

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