PoC-align: An open-source alignment accelerator using FPGAs

The mapping of reads, i.e. short DNA base pair strings, to large genome databases has become a critical operation for genetic analysis and diagnosis. The underlying alignment operation essentially is a string search tolerating some character mismatches and possibly character deletions or insertions with respect to a reference genome. Its output comprises the locations within the reference that are likely to correspond to the mapped DNA snippet. This paper describes PoC-Align, an alignment infrastructure using FPGA accelerators. It is an extension of our preceding FPGA aligner [1], which has been enhanced to tolerate alignment gaps (insertions and deletions) and to be more customizable though generic parameters. In addition to the descriptions of the implementation of these extensions, we also name the mainly software-carried enhancements, such as the support of mapping paired-end reads, that are implemented on top of the FPGA accelerator. Providing a thorough overview on the complete infrastructure, we aim at advertising the disclosure of the sources of our solution and hope to encourage other groups to use and extend this platform.