FPGA Acceleration of Sequence Alignment: A Survey

Abstract

Genomics is changing our understanding of humans, evolution, diseases, and medicines to name but a few. As sequencing technology is developed collecting DNA sequences takes less time thereby generating more genetic data every day. Today the rate of generating genetic data is outpacing the rate of computation power growth. Current sequencing machines can sequence 50 humans genome per day; however, aligning the read sequences against a reference genome and assembling the genome will take 1300 CPU hours [1]. The main step in constructing the genome is aligning the reads against a reference genome. Numerous accelerators have been proposed to accelerate the DNA alignment process. Providing massive parallelism, FPGA-based accelerators have shown great performance in accelerating DNA alignment algorithms. Additionally, FPGA-based accelerators provide better energy efficiency than general-purpose processors. In this survey, we introduce three main DNA alignment algorithms and FPGAbased implementation of these algorithms to accelerate the DNA alignment. We also, compare these three alignment categories and show how accelerators are developing during the time.

SparkFlow: Towards High-Performance Data Analytics for Spark-based Genome Analysis

“…FPGAbased solutions are accelerating the DNA alignment analysis by affording extensive parallelism and high performance. Besides, they return with better energy efficiency and reconfigurability [36]. In [35], the authors address the variant calling tool, i.e., HaplotypeCaller performance, by analyzing the PairHMM and propose an FPGA-based architecture.…”

An FPGA Accelerator of the Wavefront Algorithm for Genomics Pairwise Alignment

“…Many ASIC and FPGA-based methods have been proposed to accelerate the SW algorithm. As a result, some surveys [65]- [67] have been published summarizing the many contributions done over the years. In addition, many production-ready bioinformatics tools already incorporate custom FPGA accelerators [35]- [38], [45], [52], [53].…”

Acceleration of Short Read Alignment with Runtime Reconfiguration

“…Comprehensive surveys regarding the FPGA acceleration of short read alignment are provided in [2], [14]. Basically, many of the existing accelerators are based on the suffix-trie method, or the Smith-Waterman algorithm, or both.…”