Title |
A hybrid short read mapping accelerator
|
---|---|
Published in |
BMC Bioinformatics, February 2013
|
DOI | 10.1186/1471-2105-14-67 |
Pubmed ID | |
Authors |
Yupeng Chen, Bertil Schmidt, Douglas L Maskell |
Abstract |
The rapid growth of short read datasets poses a new challenge to the short read mapping problem in terms of sensitivity and execution speed. Existing methods often use a restrictive error model for computing the alignments to improve speed, whereas more flexible error models are generally too slow for large-scale applications. A number of short read mapping software tools have been proposed. However, designs based on hardware are relatively rare. Field programmable gate arrays (FPGAs) have been successfully used in a number of specific application areas, such as the DSP and communications domains due to their outstanding parallel data processing capabilities, making them a competitive platform to solve problems that are "inherently parallel". |
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