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Genomic Applications on Cray supercomputers : Next Generation Sequencing Workflow
| Content Provider | Semantic Scholar |
|---|---|
| Author | Kandel, Mikhail Eugene |
| Copyright Year | 2013 |
| Abstract | Recent progress in DNA sequencing technology has yielded a new class of devices that allow for the a n lysis of genetic material with unprecedented speed and effic iency. These advances, styled under the name Next-Generation Seq uencing (NGS), increasingly shift the burden from chemistry done in a laboratory to a string manipulation problem, well suited to HighPerformance Computing (HPC). By breaking up DNA into millions of small strands (20 to 1000 bases) and re ading them in parallel, the rate at which genetic material can be acquired has increased by several orders of magnitude at the exp ense of a new distinction between raw and processed genetic data. The technology that generates raw genomic data is becom ing increasingly fast and inexpensive when compared to the rate that this data can be analyzed. In general, assembling s mall reads into a useful form is done by either assembling individu al reads (de novo) or mapping these pieces against a reference (mapp ing). In this paper, we present our experience with Ray, a p arallel shortread de novo assembler code. We also present a configuration f or an NGS workflow based on Sonexion storage and Cray supercomputers. Keywords—Next-generation sequencing; assembler; DNA ; high-performance computing; parallel; genome |
| File Format | PDF HTM / HTML |
| Alternate Webpage(s) | https://cug.org/proceedings/cug2013_proceedings/includes/files/pap104.pdf |
| Language | English |
| Access Restriction | Open |
| Content Type | Text |
| Resource Type | Article |
