GMX: Instruction Set Extensions for Fast, Scalable, and Efficient Genome Sequence Alignment-Reference-Cited by-同舟云学术

GMX: Instruction Set Extensions for Fast, Scalable, and Efficient Genome Sequence Alignment

Published:2023-10-28 Issue: Volume: Page:
ISSN:
Container-title:56th Annual IEEE/ACM International Symposium on Microarchitecture
language:
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Author:

Doblas Max¹^ORCID,Lostes-Cazorla Oscar¹^ORCID,Aguado-Puig Quim²^ORCID,Cebry Nick³^ORCID,Fontova-Musté Pau¹^ORCID,Batten Christopher Frances⁴^ORCID,Marco-Sola Santiago⁵^ORCID,Moretó Miquel⁶^ORCID

Affiliation:

1. Computer Science, Barcelona Supercomputing Center (BSC), Spain

2. Dept. d'Arquitectura de Computadors i Sistemes Operatius, Universitat Autònoma de Barcelona, Spain

3. School of Electrical and Computer Engineering, Cornell University, USA

4. School of Electrical and Computer Engineering, Cornell University, United States of America

5. Computer Science, Barcelona Supercomputing Center (BSC), Spain and Computer Science, Universitat Politècnica de Catalunya, Spain

6. Computer Science, Barcelona Supercomputing Center (BSC), Spain and Computer Architecture Department, Universitat Politècnica de Catalunya, Spain

Publisher

ACM

Link

https://dl.acm.org/doi/pdf/10.1145/3613424.3614306

Reference117 articles.

1. Accelerating Edit-Distance Sequence Alignment on GPU Using the Wavefront Algorithm

2. Quim Aguado-Puig , Santiago Marco-Sola , Juan Carlos Moure , Christos Matzoros , David Castells-Rufas , Antonio Espinosa , and Miquel Moreto . 2022. WFA-GPU: Gap-affine pairwise alignment using GPUs. bioRxiv ( 2022 ). Quim Aguado-Puig, Santiago Marco-Sola, Juan Carlos Moure, Christos Matzoros, David Castells-Rufas, Antonio Espinosa, and Miquel Moreto. 2022. WFA-GPU: Gap-affine pairwise alignment using GPUs. bioRxiv (2022).

3. Nauman Ahmed , Jonathan Lévy , Shanshan Ren , Hamid Mushtaq , Koen Bertels , and Zaid Al-Ars . 2019. GASAL2: a GPU accelerated sequence alignment library for high-throughput NGS data. BMC bioinformatics 20, 1 ( 2019 ), 1–20. Nauman Ahmed, Jonathan Lévy, Shanshan Ren, Hamid Mushtaq, Koen Bertels, and Zaid Al-Ars. 2019. GASAL2: a GPU accelerated sequence alignment library for high-throughput NGS data. BMC bioinformatics 20, 1 (2019), 1–20.

4. Accelerating Genome Analysis: A Primer on an Ongoing Journey

5. Mohammed Alser , Joel Lindegger , Can Firtina , Nour Almadhoun , Haiyu Mao , Gagandeep Singh , Juan Gomez-Luna , and Onur Mutlu . 2022. From molecules to genomic variations: Accelerating genome analysis via intelligent algorithms and architectures. Computational and Structural Biotechnology Journal ( 2022 ). Mohammed Alser, Joel Lindegger, Can Firtina, Nour Almadhoun, Haiyu Mao, Gagandeep Singh, Juan Gomez-Luna, and Onur Mutlu. 2022. From molecules to genomic variations: Accelerating genome analysis via intelligent algorithms and architectures. Computational and Structural Biotechnology Journal (2022).