Inexact Search Acceleration on FPGAs Using the Burrows-Wheeler Transform

Inexact search is a difficult and time-consuming task with widespread application. Acceleration of inexact search could have tremendous impact upon fields such as chemistry, meteorology, and even bioinformatics. Field-programmable gate arrays provide a means by which to accelerate this process. We demonstrate the acceleration of inexact search using the BurrowsWheeler transform on FPGAs using the short read mapping problem in bioinformatics as an example application. Using 12 FPGAs, we are able to accelerate the search of 100-base short reads against the human genome by 48X.