Abstract
Genomic analysis has attracted a lot of interest recently since it is the key to realizing precision medicine for diseases such as cancer. Among all the genomic analysis pipeline stages, Indel Realignment is the most time-consuming and induces intensive data movements. Thus, we propose RePAIR, the first ReRAM-based processing-in-memory accelerator targeting the Indel Realignment algorithm. To further increase the computation parallelism, we design several mapping and scheduling optimization schemes. RePAIR achieves 7443× speedup and is 27211× more energy efficient over the GATK3.8 running on a CPU server, significantly outperforming the state-of-the-art.
| Original language | English |
|---|---|
| Title of host publication | Proceedings of the 2022 Design, Automation and Test in Europe Conference and Exhibition, DATE 2022 |
| Editors | Cristiana Bolchini, Ingrid Verbauwhede, Ioana Vatajelu |
| Publisher | Institute of Electrical and Electronics Engineers Inc. |
| Pages | 400-405 |
| Number of pages | 6 |
| ISBN (Electronic) | 9783981926361 |
| DOIs | |
| State | Published - 2022 |
| Externally published | Yes |
| Event | 2022 Design, Automation and Test in Europe Conference and Exhibition, DATE 2022 - Virtual, Online, Belgium Duration: 14 03 2022 → 23 03 2022 |
Publication series
| Name | Proceedings of the 2022 Design, Automation and Test in Europe Conference and Exhibition, DATE 2022 |
|---|
Conference
| Conference | 2022 Design, Automation and Test in Europe Conference and Exhibition, DATE 2022 |
|---|---|
| Country/Territory | Belgium |
| City | Virtual, Online |
| Period | 14/03/22 → 23/03/22 |
Bibliographical note
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