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

Abstract

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.

Reconfigurable acceleration of genetic sequence alignment: A survey of two decades of efforts

“…Implemented on Virtex-6 XC6VLX550T FPGA, the hardware mapper reports 2× more locations than Bowtie while maintaining the execution latency competitive to software executed on i7-2600K (4-thread). This solution is also ported onto Virtex-7 XC7VX485T and is realized as an open-source package called PoC-Align [88].…”

“…Other mentioned efforts, such as [86] and [88], are also tightly-coupled with software environment and presented as hybrid system to accelerate short-read alignment.…”