MOMS : A pipeline for scaffolding using multi-optical maps
© 2023 John Wiley & Sons Ltd..
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.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2023 |
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| Erschienen: |
2023 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:23 |
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| Enthalten in: |
Molecular ecology resources - 23(2023), 8 vom: 21. Nov., Seite 1914-1929 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Xu, Jiang [VerfasserIn] |
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| Links: |
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| Themen: |
Directed node graph |
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| Anmerkungen: |
Date Completed 04.10.2023 Date Revised 04.10.2023 published: Print-Electronic Citation Status MEDLINE |
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| doi: |
10.1111/1755-0998.13842 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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| 520 | |a 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 | ||
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| 650 | 4 | |a telomere-to-telomere assembly | |
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| 700 | 1 | |a Guo, Shuai |e verfasserin |4 aut | |
| 700 | 1 | |a Xiao, Shuiming |e verfasserin |4 aut | |
| 700 | 1 | |a Liao, Xuejiao |e verfasserin |4 aut | |
| 700 | 1 | |a Jiang, Hongshan |e verfasserin |4 aut | |
| 700 | 1 | |a Zang, Chen |e verfasserin |4 aut | |
| 700 | 1 | |a Shen, Xiaofeng |e verfasserin |4 aut | |
| 700 | 1 | |a Chu, Yang |e verfasserin |4 aut | |
| 700 | 1 | |a Wu, Wenguang |e verfasserin |4 aut | |
| 700 | 1 | |a Dou, Deqiang |e verfasserin |4 aut | |
| 700 | 1 | |a Luo, Lu |e verfasserin |4 aut | |
| 700 | 1 | |a Li, Qiushi |e verfasserin |4 aut | |
| 700 | 1 | |a Yang, Tae-Jin |e verfasserin |4 aut | |
| 700 | 1 | |a Guo, Yiming |e verfasserin |4 aut | |
| 700 | 1 | |a Huang, Zhihai |e verfasserin |4 aut | |
| 700 | 1 | |a Chen, Shilin |e verfasserin |4 aut | |
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