Conference proceeding
Towards a More Accurate Error Model for BioNano Optical Maps
BIOINFORMATICS RESEARCH AND APPLICATIONS, ISBRA 2016, v 9683, pp 67-79
01 Jan 2016
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
Next-generation sequencing technologies has advanced our knowledge in genomics by a tremendous step in the past years. On the other hand, there are still critical questions left unanswered due to the intrinsic limitations of short read length. To address this issue, several new sequencing platforms came into view. However, a lack of comprehensive understanding of the sequencing error poses a primary challenge for their optimal use. Here, we focus on optical mapping, a high-throughput laboratory technique that provides long-range information of a genome. Existing error model is based on OpGen maps. It is not clear if the model is also good for BioNano maps. In this paper, we try to provide a more accurate error model for BioNano optical maps based on real data. Due to the limited availability of real datasets, as an indirect validation of our model, we predict the regions that are difficult to cover and compare the predicted results with the empirical results (both simulated and real data) on human chromosomes. The results are promising, with most of the difficult regions correctly predicted. Tested on BioNano maps, our model is more accurate than the most popular existing error model developed based on OpGen maps. Although we may not have captured all possible errors of the technology, our model should provide important insights for the development of downstream analysis tools using BioNano optical maps.
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Details
- Title
- Towards a More Accurate Error Model for BioNano Optical Maps
- Creators
- Menglu Li - University of Hong KongAngel C. Y. Mak - University of CaliforniaErnest T. Lam - BioNano GenomicsPui-Yan Kwok - University of CaliforniaMing Xiao - Drexel UniversityKevin Y. Yip - Chinese University of Hong KongTing-Fung Chan - Chinese Univ Hong Kong, Sch Life Sci, Hong Kong, Hong Kong, Peoples R ChinaSiu-Ming Yiu - University of Hong Kong
- Contributors
- A Bourgeois (Editor)P Skums (Editor)Wan (Editor)A Zelikovsky (Editor)
- Publication Details
- BIOINFORMATICS RESEARCH AND APPLICATIONS, ISBRA 2016, v 9683, pp 67-79
- Series
- Lecture Notes in Bioinformatics
- Publisher
- Springer Nature
- Number of pages
- 13
- Resource Type
- Conference proceeding
- Language
- English
- Academic Unit
- School of Biomedical Engineering, Science, and Health Systems
- Web of Science ID
- WOS:000385788800006
- Scopus ID
- 2-s2.0-84977580390
- Other Identifier
- 991019167915604721
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- Collaboration types
- Domestic collaboration
- International collaboration
- Web of Science research areas
- Biochemical Research Methods
- Computer Science, Information Systems
- Mathematical & Computational Biology