MESGA: An MPSoC based embedded system solution for short read genome alignment

Computational needs for genome processing are often satiated by enormous servers or by cloud computers. Even though there has been some work in implementing some aspects of genome processing in GPUs and FPGAs, they are often accelerators for such servers and not stand-alone systems. In this paper, for the first time, we present a method to entirely move the alignment process to embedded processors. Such a system is useful in a variety of situations where significant networked infrastructure is not available, and where privacy is a concern. A ring pipelined processor architecture for short read alignment, based on partitioned genome references is shown. A timeout based alignment method is proposed to prevent unnecessary exhaustive search. The proposed partitioning method allows an entire human genome to be processed using small embedded processors. Experimental results show that the proposed solution speeds up the performance by approximately seven times with 16 embedded processors when compared to a linear pipelined system. It is expected that the proposed solution will to lead to a portable genome analyzing device, significantly reducing cost and testing time.