A DNA Read Alignment Accelerator Based on Computational RAM
Recent years have witnessed an increasing interest in the processing-in-memory (PIM) paradigm in computing due to its promise to improve the performance through the reduction of energy-hungry and long-latency memory accesses. Joined with the explosion of data to be processed, produced in genomics-pa...
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| Veröffentlicht in: | IEEE journal on exploratory solid-state computational devices and circuits 2020-06, Vol.6 (1), p.80-88 |
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| creator | Chowdhury, Zamshed I. Zabihi, Masoud Khatamifard, S. Karen Zhao, Zhengyang Resch, Salonik Razaviyayn, Meisam Wang, Jian-Ping Sapatnekar, Sachin S. Karpuzcu, Ulya R. |
| description | Recent years have witnessed an increasing interest in the processing-in-memory (PIM) paradigm in computing due to its promise to improve the performance through the reduction of energy-hungry and long-latency memory accesses. Joined with the explosion of data to be processed, produced in genomics-particularly genome sequencing-PIM has become a potential promising candidate for accelerating genomics applications since they do not scale up well in conventional von Neumann systems. In this article, we present an in-memory accelerator architecture for DNA read alignment. This architecture outperforms corresponding software implementation by >49X and >18 000X, in terms of throughput and energy efficiency, respectively, even under conservative assumptions. |
| doi_str_mv | 10.1109/JXCDC.2020.2987527 |
| format | Article |
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| source | IEEE Open Access Journals; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals |
| subjects | Accelerator Arrays Bioinformatics BWA computational RAM (CRAM) DNA genome sequence Genomics Indexes Memory management processing in memory (PIM) Sequential analysis spin Hall effect magnetic tunnel junction (SHE-MTJ) |
| title | A DNA Read Alignment Accelerator Based on Computational RAM |
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