GenPIP: In-Memory Acceleration of Genome Analysis via Tight Integration of Basecalling and Read Mapping

  title={GenPIP: In-Memory Acceleration of Genome Analysis via Tight Integration of Basecalling and Read Mapping},
  author={Haiyu Mao and Mohammed H. Alser and Mohammad Sadrosadati and Can Firtina and Akanksha Baranwal and Damla Senol Cali and Aditya Manglik and Nour Almadhoun Alserr and Onur Mutlu},
  journal={2022 55th IEEE/ACM International Symposium on Microarchitecture (MICRO)},
  • Haiyu MaoM. Alser O. Mutlu
  • Published 18 September 2022
  • Biology, Engineering, Computer Science
  • 2022 55th IEEE/ACM International Symposium on Microarchitecture (MICRO)
Nanopore sequencing is a widely-used high-throughput genome sequencing technology that can sequence long fragments of a genome into raw electrical signals at low cost. Nanopore sequencing requires two computationally-costly processing steps for accurate downstream genome analysis. The first step, basecalling, translates the raw electrical signals into nucleotide bases (i.e., A, C, G, T). The second step, read mapping, finds the correct location of a read in a reference genome. In existing… 

ETH 263-2210-00L Computer Architecture, Fall 2022 HW 1: Processing-in-memory (SOLUTIONS)

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