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| Content Provider | IEEE Xplore Digital Library |
|---|---|
| Author | Kun Zhao Weiguo Liu Voss, G. Muller-Wittig, W. |
| Copyright Year | 2013 |
| Description | Author affiliation: Fraunhofer IDM, Nanyang Technol. Univ., Singapore, Singapore (Voss, G.; Muller-Wittig, W.) || Sch. of Comput. Sci. & Technol., Shandong Univ., Jinan, China (Kun Zhao; Weiguo Liu) |
| Abstract | The development of next-generation sequencing technologies has revolutionized the genome research and given rise to the explosive increase of DNA sequencing throughput. However, due to the continuing explosive growth of short-read database, these technologies face the challenges of short overlap and high throughput. The de Bruijn graph is particularly suitable for short-read assemblies, and its advantage is that the graph size will not be affected by the high redundancy of deep read coverage. With this character, the fragment assembly is cast as finding a path visiting every edge in the graph exactly once. In this paper, we present a new method to accelerate the genome assembly procedure. We have used a distributed dynamic hashing approach to construct the de Bruijn graph from short-read data. Evaluations using three paired-end datasets show that, our method outperforms previous parallel and distributed assemblers on a CPU cluster system. |
| Starting Page | 1 |
| Ending Page | 4 |
| File Size | 337284 |
| Page Count | 4 |
| File Format | |
| ISBN | 9781479928255 |
| ISSN | 21593450 |
| e-ISBN | 9781479928279 |
| DOI | 10.1109/TENCON.2013.6719008 |
| Language | English |
| Publisher | Institute of Electrical and Electronics Engineers, Inc. (IEEE) |
| Publisher Date | 2013-10-22 |
| Publisher Place | China |
| Access Restriction | Subscribed |
| Rights Holder | Institute of Electrical and Electronics Engineers, Inc. (IEEE) |
| Subject Keyword | Bioinformatics Assembly Vectors Genomics Couplings Sequential analysis Acceleration Genome assembly Dynamic hashing De Bruijn graph |
| Content Type | Text |
| Resource Type | Article |
| Subject | Electrical and Electronic Engineering Computer Science Applications |
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