Reconfigurable filtered acceleration of short read alignment

Abstract

Recent trends in the cost and demand of next generation DNA sequencing (NGS) has revealed a great computational challenge in analysing the massive quantities of sequenced data produced. Given that the projected increase in sequenced data far outstrips Moore's Law, the current technologies used to handle the data are likely to become insufficient. This paper explores the use of reconfigurable hardware in accelerating short read alignment. In this application, the positions of millions of short DNA sequences (called reads) are located in a known reference genome. This work proposes a new general approach for accelerating suffix-trie based short read alignment methods using reconfigurable hardware. In the proposed approach, specialised filters are designed to align short reads to a reference genome with a specific edit distance. The filters are arranged in a pipeline according to increasing edit distance, where short reads unable to be aligned by a given filter are forwarded to the next filter in the pipeline for further processing. Run-time reconfiguration is used to fully populate an accelerator device with each filter in the pipeline in turn. In our implementation a single FPGA is populated with specialised filters based on a novel bidirectional backtracking version of the FM-index, and it is found that in this particular implementation the alignment time can be up to 14.7 and 18.1 times faster than SOAP2 and BWA run on dual Intel X5650 CPUs.