FPGA Acceleration of Pre-Alignment Filters for Short Read Mapping With HLS

David Castells-Rufas, Santiago Marco-Sola, Juan Carlos Moure, Quim Aguado, Antonio Espinosa

Research output: Contribution to journalArticleResearchpeer-review

4 Citations (Scopus)


Pre-alignment filters are useful for reducing the computational requirements of genomic sequence mappers. Most of them are based on estimating or computing the edit distance between sequences and their candidate locations in a reference genome using a subset of the dynamic programming table used to compute Levenshtein distance. Some of their FPGA implementations of use classic HDL toolchains, thus limiting their portability. Currently, most FPGA accelerators offered by heterogeneous cloud providers support C/C++ HLS. In this work, we implement and optimize several state-of-the-art pre-alignment filters using C/C++ based-HLS to expand their portability to a wide range of systems supporting the OpenCL runtime. Moreover, we perform a complete analysis of the performance and accuracy of the filters and analyze the implications of the results. The maximum throughput obtained by an exact filter is 95.1 MPairs/s including memory transfers using 100 bp sequences, which is the highest ever reported for a comparable system and more than two times faster than previous HDL-based results. The best energy efficiency obtained from the accelerator (not considering host CPU) is 2.1 MPairs/J, more than one order of magnitude higher than other accelerator-based comparable approaches from the state of the art.

Original languageEnglish
Pages (from-to)22079-22100
Number of pages22
JournalIEEE Access
Publication statusPublished - 21 Feb 2022


  • Field programmable gate arrays
  • OpenCL
  • acceleration
  • bioinformatics
  • hardware
  • pre-alignment filters
  • read mapping
  • sequence alignment


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