RawHash: Enabling Fast and Accurate Real-Time Analysis of Raw Nanopore Signals for Large Genomes

1 code implementation • 22 Jan 2023 • Can Firtina, Nika Mansouri Ghiasi, Joel Lindegger, Gagandeep Singh, Meryem Banu Cavlak, Haiyu Mao, Onur Mutlu

An important feature of nanopore sequencing, Read Until, can eject strands from sequencers without fully sequencing them, which provides opportunities to computationally reduce the sequencing time and cost.

Quantization

TargetCall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling Filtering

1 code implementation • 9 Dec 2022 • Meryem Banu Cavlak, Gagandeep Singh, Mohammed Alser, Can Firtina, Joël Lindegger, Mohammad Sadrosadati, Nika Mansouri Ghiasi, Can Alkan, Onur Mutlu

However, for many applications, the majority of reads do no match the reference genome of interest (i. e., target reference) and thus are discarded in later steps in the genomics pipeline, wasting the basecalling computation.

BLEND: A Fast, Memory-Efficient, and Accurate Mechanism to Find Fuzzy Seed Matches in Genome Analysis

1 code implementation • 16 Dec 2021 • Can Firtina, Jisung Park, Mohammed Alser, Jeremie S. Kim, Damla Senol Cali, Taha Shahroodi, Nika Mansouri Ghiasi, Gagandeep Singh, Konstantinos Kanellopoulos, Can Alkan, Onur Mutlu

We introduce BLEND, the first efficient and accurate mechanism that can identify both exact-matching and highly similar seeds with a single lookup of their hash values, called fuzzy seeds matches.

SIMDRAM: A Framework for Bit-Serial SIMD Processing Using DRAM

no code implementations • 22 Dec 2020 • Nastaran Hajinazar, Geraldo F. Oliveira, Sven Gregorio, João Dinis Ferreira, Nika Mansouri Ghiasi, Minesh Patel, Mohammed Alser, Saugata Ghose, Juan Gómez-Luna, Onur Mutlu

Compared to a CPU and a high-end GPU, SIMDRAM is 257x and 31x more energy-efficient, while providing 93x and 6x higher operation throughput, respectively.

Hardware Architecture Distributed, Parallel, and Cluster Computing Emerging Technologies