Title |
Using optical mapping data for the improvement of vertebrate genome assemblies
|
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Published in |
Giga Science, March 2015
|
DOI | 10.1186/s13742-015-0052-y |
Pubmed ID | |
Authors |
Kerstin Howe, Jonathan MD Wood |
Abstract |
Optical mapping is a technology that gathers long-range information on genome sequences similar to ordered restriction digest maps. Because it is not subject to cloning, amplification, hybridisation or sequencing bias, it is ideally suited to the improvement of fragmented genome assemblies that can no longer be improved by classical methods. In addition, its low cost and rapid turnaround make it equally useful during the scaffolding process of de novo assembly from high throughput sequencing reads. We describe how optical mapping has been used in practice to produce high quality vertebrate genome assemblies. In particular, we detail the efforts undertaken by the Genome Reference Consortium (GRC), which maintains the reference genomes for human, mouse, zebrafish and chicken, and uses different optical mapping platforms for genome curation. |
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United Kingdom | 3 | 12% |
Canada | 2 | 8% |
France | 2 | 8% |
Germany | 1 | 4% |
Norway | 1 | 4% |
India | 1 | 4% |
Hong Kong | 1 | 4% |
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Demographic breakdown
Type | Count | As % |
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Scientists | 14 | 56% |
Members of the public | 10 | 40% |
Science communicators (journalists, bloggers, editors) | 1 | 4% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Netherlands | 3 | 2% |
United States | 3 | 2% |
Norway | 2 | 2% |
Germany | 1 | <1% |
Brazil | 1 | <1% |
Hong Kong | 1 | <1% |
Mexico | 1 | <1% |
United Kingdom | 1 | <1% |
Unknown | 109 | 89% |
Demographic breakdown
Readers by professional status | Count | As % |
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Researcher | 29 | 24% |
Student > Bachelor | 10 | 8% |
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Professor > Associate Professor | 8 | 7% |
Other | 18 | 15% |
Unknown | 11 | 9% |
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Computer Science | 7 | 6% |
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Physics and Astronomy | 3 | 2% |
Other | 5 | 4% |
Unknown | 13 | 11% |