Papers, reviews, tutorials

2020

1. IEEE Micro

   Accelerating Genome Analysis: A Primer on an Ongoing Journey

   Mohammed Alser, Zülal Bingöl, Damla Senol Cali, Jeremie Kim, Saugata Ghose, Can Alkan, and Onur Mutlu

   IEEE Micro, 2020

   Abstract BIB URL

   Genome analysis fundamentally starts with a process known as read mapping, where sequenced fragments of an organism’s genome are compared against a reference genome. Read mapping is currently a major bottleneck in the entire genome analysis pipeline, because state-of-the-art genome sequencing technologies are able to sequence a genome much faster than the computational techniques employed to analyze the genome. We describe the ongoing journey in significantly improving the performance of read mapping. We explain state-of-the-art algorithmic methods and hardware-based acceleration approaches. Algorithmic approaches exploit the structure of the genome as well as the structure of the underlying hardware. Hardware-based acceleration approaches exploit specialized microarchitectures or various execution paradigms (e.g., processing inside or near memory). We conclude with the challenges of adopting these hardware-accelerated read mappers.

   @article{alser_accelerating_2020,
     title = {Accelerating {Genome} {Analysis}: {A} {Primer} on an {Ongoing} {Journey}},
     volume = {40},
     doi = {10.1109/MM.2020.3013728},
     number = {5},
     journal = {IEEE Micro},
     author = {Alser, Mohammed and Bingöl, Zülal and Cali, Damla Senol and Kim, Jeremie and Ghose, Saugata and Alkan, Can and Mutlu, Onur},
     year = {2020},
     pages = {65--75},
   }