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Syst."],"published-print":{"date-parts":[[2023,12,31]]},"abstract":"<jats:p>In genome analysis, it is often important to identify variants from a reference genome. However, identifying variants that occur with low frequency can be challenging, as it is computationally intensive to do so accurately. LoFreq is a widely used program that is adept at identifying low-frequency variants. This article presents a design framework for an FPGA-based accelerator for LoFreq. In particular, this accelerator is targeted at virus analysis, which is particularly challenging, compared to human genome analysis, as the characteristics of the data to be analyzed are fundamentally different. Across the design space, this accelerator can achieve up to 120\u00d7 speedups on the core computation of LoFreq and speedups of up to 51.7\u00d7 across the entire program.<\/jats:p>","DOI":"10.1145\/3595297","type":"journal-article","created":{"date-parts":[[2023,5,22]],"date-time":"2023-05-22T12:04:21Z","timestamp":1684757061000},"page":"1-29","update-policy":"https:\/\/doi.org\/10.1145\/crossmark-policy","source":"Crossref","is-referenced-by-count":4,"title":["An FPGA Accelerator for Genome Variant Calling"],"prefix":"10.1145","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8817-7094","authenticated-orcid":false,"given":"Tiancheng","family":"Xu","sequence":"first","affiliation":[{"name":"Rice University, USA"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-5204-742X","authenticated-orcid":false,"given":"Scott","family":"Rixner","sequence":"additional","affiliation":[{"name":"Rice University, USA"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-4904-9600","authenticated-orcid":false,"given":"Alan L.","family":"Cox","sequence":"additional","affiliation":[{"name":"Rice University, USA"}]}],"member":"320","published-online":{"date-parts":[[2023,9]]},"reference":[{"key":"e_1_3_1_2_2","unstructured":"R Accelerating Genomics Research with OpenCL and FPGAs"},{"key":"e_1_3_1_3_2","unstructured":"R GPU-Accelerated Tools Added to NVIDIA Clara Parabricks v3.6 for Cancer and Germline Analyses"},{"key":"e_1_3_1_4_2","unstructured":"Retrieved from January 15 2022 NCBI SARS-CoV-2 Resources"},{"key":"e_1_3_1_5_2","unstructured":"Retrieved from January 14 2022 Nvidia Clara Parabricks Documentation"},{"key":"e_1_3_1_6_2","unstructured":"Retrieved from January 14 2022 Source Code Repository of LoFreq"},{"key":"e_1_3_1_7_2","unstructured":"Retrieved from April 7 2022 Vivado Design Suite User Guide - Implementation"},{"key":"e_1_3_1_8_2","unstructured":"Retrieved from January 15 2022 Xilinx Alveo U250 Accelerator Card"},{"key":"e_1_3_1_9_2","unstructured":"Retrieved from April 7 2022 Xilinx Large FPGA Methodology Guide"},{"key":"e_1_3_1_10_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btaa1015"},{"key":"e_1_3_1_11_2","doi-asserted-by":"publisher","DOI":"10.1109\/TCBB.2016.2535385"},{"key":"e_1_3_1_12_2","doi-asserted-by":"publisher","DOI":"10.23919\/FPL.2017.8056837"},{"key":"e_1_3_1_13_2","doi-asserted-by":"publisher","DOI":"10.1109\/IPDPSW52791.2021.00039"},{"key":"e_1_3_1_14_2","doi-asserted-by":"publisher","DOI":"10.1093\/imanum\/draa038"},{"key":"e_1_3_1_15_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-21361-7"},{"key":"e_1_3_1_16_2","doi-asserted-by":"publisher","DOI":"10.1109\/FCCM.2016.21"},{"key":"e_1_3_1_17_2","doi-asserted-by":"publisher","DOI":"10.1109\/FCCM.2015.27"},{"key":"e_1_3_1_18_2","first-page":"2020.07.27.2234","article-title":"Oligonucleotide capture sequencing of the SARS-CoV-2 genome and subgenomic fragments from COVID-19 individuals","author":"Doddapaneni Harsha","year":"2020","unstructured":"Harsha Doddapaneni, Sara Javornik Cregeen, Richard Sucgang, Qingchang Meng, Xiang Qin, Vasanthi Avadhanula, Hsu Chao, Vipin Menon, Erin Nicholson, David Henke, Felipe-Andres Piedra, Anubama Rajan, Zeineen Momin, Kavya Kottapalli, Kristi L. Hoffman, Fritz J. Sedlazeck, Ginger Metcalf, Pedro A. Piedra, Donna M. Muzny, Joseph F. Petrosino, and Richard A. Gibbs. 2020. Oligonucleotide capture sequencing of the SARS-CoV-2 genome and subgenomic fragments from COVID-19 individuals. bioRxiv: The preprint server for biology (27 July 2020), 2020.07.27.223495.","journal-title":"bioRxiv: The preprint server for biology"},{"key":"e_1_3_1_19_2","doi-asserted-by":"publisher","DOI":"10.1109\/ISCA.2018.00017"},{"key":"e_1_3_1_20_2","doi-asserted-by":"publisher","DOI":"10.1109\/MICRO50266.2020.00080"},{"key":"e_1_3_1_21_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-018-1618-7"},{"key":"e_1_3_1_22_2","doi-asserted-by":"publisher","DOI":"10.1109\/FCCM.2019.00027"},{"key":"e_1_3_1_23_2","first-page":"275","volume-title":"ACM\/SIGDA International Symposium on Field-Programmable Gate Arrays","author":"Huang Sitao","year":"2017","unstructured":"Sitao Huang, Gowthami Jayashri Manikandan, Anand Ramachandran, Kyle Rupnow, Wen-mei W. 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