A Survey of Processing Systems for Phylogenetics and Population Genetics

The COVID-19 pandemic brought Bioinformatics into the spotlight, revealing that several existing methods, algorithms, and tools were not well prepared to handle large amounts of genomic data efficiently. This led to prohibitively long execution times and the need to reduce the extent of analyses to obtain results in a reasonable amount of time. In this survey, we review available high-performance computing and hardware-accelerated systems based on FPGA and GPU technology. Optimized and hardware-accelerated systems can conduct more thorough analyses considerably faster than pure software implementations, allowing to reach important conclusions in a timely manner to drive scientific discoveries. We discuss the reasons that are currently hindering high-performance solutions from being widely deployed in real-world biological analyses and describe a research direction that can pave the way to enable this.

• Publication year

  2023

• Venue

  ACM Transactions on Reconfigurable Technology and Systems

• Publication date

  2023-03-16

• Fields of study

  Biology, Computer Science

• Identifiers
  DOI 10.1145/3588033
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar

• No claims are published for this paper.

• No concepts are published for this paper.

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