DNA assembly with de bruijn graphs on FPGA.

Publication Type:

Journal Article

Authors:

Poirier, Carl; Benoit Gosselin; Fortier, Paul

Source:

Conf Proc IEEE Eng Med Biol Soc, Volume 2015, p.6489-92 (2015)

Keywords:

Acceleration, Algorithms, Computational Biology, Computer Graphics, DNA, Genome, Programming Languages, Sequence Analysis, DNA, Software

Abstract:

<p>This project aims to see if accelerators based on FPGAs are worthwhile for DNA assembly. It involves reprogramming an already existing algorithm - called Ray - to be run either on such an accelerator or on a CPU to be able to compare both. It has been achieved using the OpenCL language. The focus is put on modifying and optimizing the original algorithm to better suit the new parallelization tool. Upon running the new program on some datasets, it becomes clear that FPGAs are a very capable platform that can fare better than the traditional approach, both on raw performance and energy consumption. </p>