Using optical mapping data for the improvement of vertebrate genome assemblies

GigaScience

Jonathan MD Wood¹  Kerstin Howe¹ 

[1] Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus Hinxton, Cambridge, UK

关键词: Rmap;    genome assembly;    reference genomes;    Genome Reference Consortium;    Optical mapping;   

Others  :  1149289
DOI  :  10.1186/s13742-015-0052-y

 received in 2014-12-17, accepted in 2015-03-05,  发布年份 2015

【 摘 要 】

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.

【 授权许可】

   
2015 Howe and Wood; licensee BioMed Central.

【 图 表 】

Figure 1.

Figure 2.

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