A CUDA-based Implementation of the SSAKE Genomics Application

Present advances in sequencing technology make possible to generate large amounts of data in short time. However one major issue is represented by the fact that fragments produced by these high-throughput methods are short and in very high number, resulting in a difficult analytical task. Two different approaches are currently applied to genome assembly, overlap graph and sequence hashing. In particular SSAKE, one of the first and more popular implementation of the sequence hashing algorithm, was designed to leverage the information from short sequence reads by stringently assembling them into contiguous sequences that can be used to characterize novel sequencing targets. In this paper we present an implementation of this tool for the CUDA architecture.