{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,5]],"date-time":"2026-03-05T15:44:35Z","timestamp":1772725475651,"version":"3.50.1"},"publisher-location":"New York, NY, USA","reference-count":63,"publisher":"ACM","license":[{"start":{"date-parts":[[2021,10,17]],"date-time":"2021-10-17T00:00:00Z","timestamp":1634428800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-sa\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["2030454"],"award-info":[{"award-number":["2030454"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Kahn Foundation"}],"content-domain":{"domain":["dl.acm.org"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2021,10,18]]},"DOI":"10.1145\/3466752.3480117","type":"proceedings-article","created":{"date-parts":[[2021,10,17]],"date-time":"2021-10-17T19:12:05Z","timestamp":1634497925000},"page":"535-549","update-policy":"https:\/\/doi.org\/10.1145\/crossmark-policy","source":"Crossref","is-referenced-by-count":36,"title":["SquiggleFilter: An Accelerator for Portable Virus Detection"],"prefix":"10.1145","author":[{"given":"Tim","family":"Dunn","sequence":"first","affiliation":[{"name":"University of Michigan, United States of America"}]},{"given":"Harisankar","family":"Sadasivan","sequence":"additional","affiliation":[{"name":"University of Michigan"}]},{"given":"Jack","family":"Wadden","sequence":"additional","affiliation":[{"name":"University of Michigan, United States of America"}]},{"given":"Kush","family":"Goliya","sequence":"additional","affiliation":[{"name":"University of Michigan, United States of America"}]},{"given":"Kuan-Yu","family":"Chen","sequence":"additional","affiliation":[{"name":"University of Michigan"}]},{"given":"David","family":"Blaauw","sequence":"additional","affiliation":[{"name":"University of Michigan"}]},{"given":"Reetuparna","family":"Das","sequence":"additional","affiliation":[{"name":"University of Michigan, United States of America"}]},{"given":"Satish","family":"Narayanasamy","sequence":"additional","affiliation":[{"name":"University of Michigan, United States of America"}]}],"member":"320","published-online":{"date-parts":[[2021,10,17]]},"reference":[{"key":"e_1_3_2_1_1_1","unstructured":"Abbott. 2021. Navica App and BinaxNOW COVID-19 Ag Test Card. https:\/\/www.globalpointofcare.abbott\/en\/product-details\/navica-binaxnow-covid-19-us.html Abbott Point of Care Testing.  Abbott. 2021. Navica App and BinaxNOW COVID-19 Ag Test Card. https:\/\/www.globalpointofcare.abbott\/en\/product-details\/navica-binaxnow-covid-19-us.html Abbott Point of Care Testing."},{"key":"e_1_3_2_1_2_1","volume-title":"KDD workshop, Vol.\u00a010","author":"Berndt J","year":"1994","unstructured":"Donald\u00a0 J Berndt and James Clifford . 1994 . Using dynamic time warping to find patterns in time series .. In KDD workshop, Vol.\u00a010 . Seattle, WA, USA:, 359\u2013370. Donald\u00a0J Berndt and James Clifford. 1994. Using dynamic time warping to find patterns in time series.. In KDD workshop, Vol.\u00a010. Seattle, WA, USA:, 359\u2013370."},{"key":"e_1_3_2_1_3_1","unstructured":"Clive Brown. 2019. Technology Update. (2019). https:\/\/nanoporetech.com\/resource-centre\/nanopore-community-meeting-2019-technology-update Nanopore Community Meeting.  Clive Brown. 2019. Technology Update. (2019). https:\/\/nanoporetech.com\/resource-centre\/nanopore-community-meeting-2019-technology-update Nanopore Community Meeting."},{"key":"e_1_3_2_1_4_1","unstructured":"CADDE. 2020. Brazil-UK Centre for Arbovirus Discovery Diagnosis Genomics and Epidemiology. https:\/\/cadde.s3.climb.ac.uk\/SP1-raw.tgz  CADDE. 2020. Brazil-UK Centre for Arbovirus Discovery Diagnosis Genomics and Epidemiology. https:\/\/cadde.s3.climb.ac.uk\/SP1-raw.tgz"},{"key":"e_1_3_2_1_5_1","volume-title":"Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis. In 2020 53rd Annual IEEE\/ACM International Symposium on Microarchitecture (MICRO). IEEE, 951\u2013966","author":"Cali Damla\u00a0Senol","year":"2020","unstructured":"Damla\u00a0Senol Cali , Gurpreet\u00a0 S Kalsi , Z\u00fclal Bing\u00f6l , Can Firtina , Lavanya Subramanian , Jeremie\u00a0 S Kim , Rachata Ausavarungnirun , Mohammed Alser , Juan Gomez-Luna , Amirali Boroumand , 2020 . GenASM: A High-Performance , Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis. In 2020 53rd Annual IEEE\/ACM International Symposium on Microarchitecture (MICRO). IEEE, 951\u2013966 . Damla\u00a0Senol Cali, Gurpreet\u00a0S Kalsi, Z\u00fclal Bing\u00f6l, Can Firtina, Lavanya Subramanian, Jeremie\u00a0S Kim, Rachata Ausavarungnirun, Mohammed Alser, Juan Gomez-Luna, Amirali Boroumand, 2020. GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis. In 2020 53rd Annual IEEE\/ACM International Symposium on Microarchitecture (MICRO). IEEE, 951\u2013966."},{"key":"e_1_3_2_1_6_1","first-page":"1","article-title":"Real-time Selective Sequencing with RUBRIC: Read until with basecall and reference-informed criteria","volume":"9","author":"Edwards S","year":"2019","unstructured":"Harrison\u00a0 S Edwards , Raga Krishnakumar , Anupama Sinha , Sara\u00a0 W Bird , Kamlesh\u00a0 D Patel , and Michael\u00a0 S Bartsch . 2019 . Real-time Selective Sequencing with RUBRIC: Read until with basecall and reference-informed criteria . Scientific Reports 9 , 1 (2019), 1 \u2013 11 . Harrison\u00a0S Edwards, Raga Krishnakumar, Anupama Sinha, Sara\u00a0W Bird, Kamlesh\u00a0D Patel, and Michael\u00a0S Bartsch. 2019. Real-time Selective Sequencing with RUBRIC: Read until with basecall and reference-informed criteria. Scientific Reports 9, 1 (2019), 1\u201311.","journal-title":"Scientific Reports"},{"key":"e_1_3_2_1_7_1","volume-title":"Real-time selective sequencing with RUBRIC: read until with basecall and reference-informed criteria. Scientific reports 9, 1","author":"Edwards S","year":"2019","unstructured":"Harrison\u00a0 S Edwards , Raga Krishnakumar , Anupama Sinha , Sara\u00a0 W Bird , Kamlesh\u00a0 D Patel , and Michael\u00a0 S Bartsch . 2019. Real-time selective sequencing with RUBRIC: read until with basecall and reference-informed criteria. Scientific reports 9, 1 ( 2019 ), 1\u201311. Harrison\u00a0S Edwards, Raga Krishnakumar, Anupama Sinha, Sara\u00a0W Bird, Kamlesh\u00a0D Patel, and Michael\u00a0S Bartsch. 2019. Real-time selective sequencing with RUBRIC: read until with basecall and reference-informed criteria. Scientific reports 9, 1 (2019), 1\u201311."},{"key":"e_1_3_2_1_8_1","doi-asserted-by":"publisher","DOI":"10.1109\/ISCA.2018.00017"},{"key":"e_1_3_2_1_9_1","volume-title":"SeedEx: A Genome Sequencing Accelerator for Optimal Alignments in Subminimal Space. In 2020 53rd Annual IEEE\/ACM International Symposium on Microarchitecture (MICRO). IEEE, 937\u2013950","author":"Fujiki Daichi","year":"2020","unstructured":"Daichi Fujiki , Shunhao Wu , Nathan Ozog , Kush Goliya , David Blaauw , Satish Narayanasamy , and Reetuparna Das . 2020 . SeedEx: A Genome Sequencing Accelerator for Optimal Alignments in Subminimal Space. In 2020 53rd Annual IEEE\/ACM International Symposium on Microarchitecture (MICRO). IEEE, 937\u2013950 . Daichi Fujiki, Shunhao Wu, Nathan Ozog, Kush Goliya, David Blaauw, Satish Narayanasamy, and Reetuparna Das. 2020. SeedEx: A Genome Sequencing Accelerator for Optimal Alignments in Subminimal Space. In 2020 53rd Annual IEEE\/ACM International Symposium on Microarchitecture (MICRO). IEEE, 937\u2013950."},{"key":"e_1_3_2_1_10_1","volume-title":"An easy, reliable and rapid SARS-CoV2 RT-LAMP based test for Point-of-Care and diagnostic lab. medRxiv","author":"AR GOUILH","year":"2020","unstructured":"Meriadeg\u00a0 AR GOUILH , Renaud CASSIER, Elodie MAILLE , Cecile Schanen , Louis-Marie ROCQUE, and Astrid VABRET. 2020. An easy, reliable and rapid SARS-CoV2 RT-LAMP based test for Point-of-Care and diagnostic lab. medRxiv ( 2020 ). Meriadeg\u00a0AR GOUILH, Renaud CASSIER, Elodie MAILLE, Cecile Schanen, Louis-Marie ROCQUE, and Astrid VABRET. 2020. An easy, reliable and rapid SARS-CoV2 RT-LAMP based test for Point-of-Care and diagnostic lab. medRxiv (2020)."},{"key":"e_1_3_2_1_11_1","volume-title":"Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis. Genome medicine 7, 1","author":"Greninger L","year":"2015","unstructured":"Alexander\u00a0 L Greninger , Samia\u00a0 N Naccache , Scot Federman , Guixia Yu , Placide Mbala , Vanessa Bres , Doug Stryke , Jerome Bouquet , Sneha Somasekar , Jeffrey\u00a0 M Linnen , 2015. Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis. Genome medicine 7, 1 ( 2015 ), 99. Alexander\u00a0L Greninger, Samia\u00a0N Naccache, Scot Federman, Guixia Yu, Placide Mbala, Vanessa Bres, Doug Stryke, Jerome Bouquet, Sneha Somasekar, Jeffrey\u00a0M Linnen, 2015. Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis. Genome medicine 7, 1 (2015), 99."},{"key":"e_1_3_2_1_12_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty407"},{"key":"e_1_3_2_1_13_1","doi-asserted-by":"publisher","DOI":"10.1109\/ISCA45697.2020.00031"},{"key":"e_1_3_2_1_14_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty555"},{"key":"e_1_3_2_1_15_1","volume-title":"A cross-country database of COVID-19 testing. Scientific data 7, 1","author":"Hasell Joe","year":"2020","unstructured":"Joe Hasell , Edouard Mathieu , Diana Beltekian , Bobbie Macdonald , Charlie Giattino , Esteban Ortiz-Ospina , Max Roser , and Hannah Ritchie . 2020. A cross-country database of COVID-19 testing. Scientific data 7, 1 ( 2020 ), 1\u20137. Joe Hasell, Edouard Mathieu, Diana Beltekian, Bobbie Macdonald, Charlie Giattino, Esteban Ortiz-Ospina, Max Roser, and Hannah Ritchie. 2020. A cross-country database of COVID-19 testing. Scientific data 7, 1 (2020), 1\u20137."},{"key":"e_1_3_2_1_16_1","volume-title":"LamPORE: rapid, accurate and highly scalable molecular screening for SARS-CoV-2 infection, based on nanopore sequencing. medRxiv","author":"James Phillip","year":"2020","unstructured":"Phillip James , David Stoddart , Eoghan\u00a0 D Harrington , John Beaulaurier , Lynn Ly , Stuart Reid , Daniel\u00a0 J Turner , and Sissel Juul . 2020. LamPORE: rapid, accurate and highly scalable molecular screening for SARS-CoV-2 infection, based on nanopore sequencing. medRxiv ( 2020 ). Phillip James, David Stoddart, Eoghan\u00a0D Harrington, John Beaulaurier, Lynn Ly, Stuart Reid, Daniel\u00a0J Turner, and Sissel Juul. 2020. LamPORE: rapid, accurate and highly scalable molecular screening for SARS-CoV-2 infection, based on nanopore sequencing. medRxiv (2020)."},{"key":"e_1_3_2_1_17_1","doi-asserted-by":"crossref","unstructured":"Eamonn Keogh and Shruti Kasetty. 2003. On the need for time series data mining benchmarks: a survey and empirical demonstration. Data Mining and knowledge discovery 7 4 349\u2013371.  Eamonn Keogh and Shruti Kasetty. 2003. On the need for time series data mining benchmarks: a survey and empirical demonstration. Data Mining and knowledge discovery 7 4 349\u2013371.","DOI":"10.1023\/A:1024988512476"},{"key":"e_1_3_2_1_18_1","unstructured":"S\u00a0Karen Khatamifard Zamshed Chowdhury Nakul Pande Meisam Razaviyayn Chris Kim and Ulya\u00a0R Karpuzcu. 2017. A non-volatile near-memory read mapping accelerator. arXiv preprint arXiv:1709.02381(2017).  S\u00a0Karen Khatamifard Zamshed Chowdhury Nakul Pande Meisam Razaviyayn Chris Kim and Ulya\u00a0R Karpuzcu. 2017. A non-volatile near-memory read mapping accelerator. arXiv preprint arXiv:1709.02381(2017)."},{"key":"e_1_3_2_1_19_1","unstructured":"Duncan Kilburn Jeff Burke Renee Fedak Hugh Olsen Miten Jain Karen Miga Simon Mayes and Kelvin Liu. [n. d.]. High Data Throughput and Low Cost Ultra Long Nanopore Sequencing. https:\/\/15a13b02-7dac-4315-baa5-b3ced1ea969d.filesusr.com\/ugd\/5518db_164bac27f4654b1f94d3472f09372498.pdf  Duncan Kilburn Jeff Burke Renee Fedak Hugh Olsen Miten Jain Karen Miga Simon Mayes and Kelvin Liu. [n. d.]. High Data Throughput and Low Cost Ultra Long Nanopore Sequencing. https:\/\/15a13b02-7dac-4315-baa5-b3ced1ea969d.filesusr.com\/ugd\/5518db_164bac27f4654b1f94d3472f09372498.pdf"},{"key":"e_1_3_2_1_20_1","volume-title":"Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED. BioRxiv","author":"Kovaka Sam","year":"2020","unstructured":"Sam Kovaka , Yunfan Fan , Bohan Ni , Winston Timp , and Michael\u00a0 C Schatz . 2020. Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED. BioRxiv ( 2020 ). Sam Kovaka, Yunfan Fan, Bohan Ni, Winston Timp, and Michael\u00a0C Schatz. 2020. Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED. BioRxiv (2020)."},{"key":"e_1_3_2_1_21_1","unstructured":"LGC. 2021. 2019-nCoV CDC-qualified Probe and Primer Kits for SARS-CoV-2. https:\/\/www.biosearchtech.com\/products\/pcr-kits-and-reagents\/pathogen-detection\/2019-ncov-cdc-probe-and-primer-kit-for-sars-cov-2 LGC Biosearch Technologies.  LGC. 2021. 2019-nCoV CDC-qualified Probe and Primer Kits for SARS-CoV-2. https:\/\/www.biosearchtech.com\/products\/pcr-kits-and-reagents\/pathogen-detection\/2019-ncov-cdc-probe-and-primer-kit-for-sars-cov-2 LGC Biosearch Technologies."},{"key":"e_1_3_2_1_22_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty191"},{"key":"e_1_3_2_1_23_1","volume-title":"A complete bacterial genome assembled de novo using only nanopore sequencing data. Nature methods 12, 8","author":"Loman J","year":"2015","unstructured":"Nicholas\u00a0 J Loman , Joshua Quick , and Jared\u00a0 T Simpson . 2015. A complete bacterial genome assembled de novo using only nanopore sequencing data. Nature methods 12, 8 ( 2015 ), 733\u2013735. Nicholas\u00a0J Loman, Joshua Quick, and Jared\u00a0T Simpson. 2015. A complete bacterial genome assembled de novo using only nanopore sequencing data. Nature methods 12, 8 (2015), 733\u2013735."},{"key":"e_1_3_2_1_24_1","volume-title":"Real-time selective sequencing using nanopore technology. Nature methods 13, 9","author":"Loose Matthew","year":"2016","unstructured":"Matthew Loose , Sunir Malla , and Michael Stout . 2016. Real-time selective sequencing using nanopore technology. Nature methods 13, 9 ( 2016 ), 751. Matthew Loose, Sunir Malla, and Michael Stout. 2016. Real-time selective sequencing using nanopore technology. Nature methods 13, 9 (2016), 751."},{"key":"e_1_3_2_1_25_1","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.31955"},{"key":"e_1_3_2_1_26_1","series-title":"Series B: Biological Sciences 359, 1447","volume-title":"Environmental and social influences on emerging infectious diseases: past, present and future. Philosophical Transactions of the Royal Society of London","author":"McMichael J","year":"2004","unstructured":"Anthony\u00a0 J McMichael . 2004. Environmental and social influences on emerging infectious diseases: past, present and future. Philosophical Transactions of the Royal Society of London . Series B: Biological Sciences 359, 1447 ( 2004 ), 1049\u20131058. Anthony\u00a0J McMichael. 2004. Environmental and social influences on emerging infectious diseases: past, present and future. Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 359, 1447 (2004), 1049\u20131058."},{"key":"e_1_3_2_1_27_1","doi-asserted-by":"crossref","unstructured":"Gage Moreno and David O\u2019Connor. 2020. Sequence-Independent Single-Primer Amplification of RNA viruses V.3. https:\/\/www.protocols.io\/view\/sequence-independent-single-primer-amplification-o-bckxiuxn.html University of Wisconsin-Madison.  Gage Moreno and David O\u2019Connor. 2020. Sequence-Independent Single-Primer Amplification of RNA viruses V.3. https:\/\/www.protocols.io\/view\/sequence-independent-single-primer-amplification-o-bckxiuxn.html University of Wisconsin-Madison.","DOI":"10.17504\/protocols.io.bckxiuxn"},{"key":"e_1_3_2_1_28_1","doi-asserted-by":"publisher","DOI":"10.1145\/3352460.3358308"},{"key":"e_1_3_2_1_29_1","unstructured":"Mayu Nagura-Ikeda Kazuo Imai Sakiko Tabata Kazuyasu Miyoshi Nami Murahara Tsukasa Mizuno Midori Horiuchi Kento Kato Yoshitaka Imoto Maki Iwata 2020. Clinical evaluation of self-collected saliva by RT-qPCR direct RT-qPCR RT-LAMP and a rapid antigen test to diagnose COVID-19. Journal of Clinical Microbiology(2020).  Mayu Nagura-Ikeda Kazuo Imai Sakiko Tabata Kazuyasu Miyoshi Nami Murahara Tsukasa Mizuno Midori Horiuchi Kento Kato Yoshitaka Imoto Maki Iwata 2020. Clinical evaluation of self-collected saliva by RT-qPCR direct RT-qPCR RT-LAMP and a rapid antigen test to diagnose COVID-19. Journal of Clinical Microbiology(2020)."},{"key":"e_1_3_2_1_30_1","unstructured":"NEB. 2021. SARS-CoV-2 Rapid Colorimetric LAMP Assay Kit. https:\/\/www.neb.com\/products\/e2019-sars-cov-2-rapid-colorimetric-lamp-assay-kit New England Biolabs.  NEB. 2021. SARS-CoV-2 Rapid Colorimetric LAMP Assay Kit. https:\/\/www.neb.com\/products\/e2019-sars-cov-2-rapid-colorimetric-lamp-assay-kit New England Biolabs."},{"key":"e_1_3_2_1_31_1","unstructured":"NVIDIA. [n. d.]. Jetson AGX Xavier Developer Kit. https:\/\/developer.nvidia.com\/embedded\/jetson-agx-xavier-developer-kit  NVIDIA. [n. d.]. Jetson AGX Xavier Developer Kit. https:\/\/developer.nvidia.com\/embedded\/jetson-agx-xavier-developer-kit"},{"key":"e_1_3_2_1_32_1","unstructured":"ONT. 2020. Metagenomic analysis of SARS-CoV-2 respiratory samples via Sequence-Independent Single Primer Amplification (SISPA) and nanopore sequencing. https:\/\/nanoporetech.com\/sites\/default\/files\/s3\/literature\/COVID-19_metagenomic_sequencing.pdf Oxford Nanopore Technologies.  ONT. 2020. Metagenomic analysis of SARS-CoV-2 respiratory samples via Sequence-Independent Single Primer Amplification (SISPA) and nanopore sequencing. https:\/\/nanoporetech.com\/sites\/default\/files\/s3\/literature\/COVID-19_metagenomic_sequencing.pdf Oxford Nanopore Technologies."},{"key":"e_1_3_2_1_33_1","unstructured":"ONT. 2020. ont-fast5-api. https:\/\/pypi.org\/project\/ont-fast5-api\/ FAST5 API: a simple interface to HDF5 files of the Oxford Nanopore.fast5 file format.  ONT. 2020. ont-fast5-api. https:\/\/pypi.org\/project\/ont-fast5-api\/ FAST5 API: a simple interface to HDF5 files of the Oxford Nanopore.fast5 file format."},{"key":"e_1_3_2_1_34_1","unstructured":"ONT. 2020. ont-pyguppy-client-lib. https:\/\/pypi.org\/project\/ont-pyguppy-client-lib\/ PyGuppy: Python bindings for the GuppyClient library.  ONT. 2020. ont-pyguppy-client-lib. https:\/\/pypi.org\/project\/ont-pyguppy-client-lib\/ PyGuppy: Python bindings for the GuppyClient library."},{"key":"e_1_3_2_1_35_1","unstructured":"ONT. 2021. cDNA PCR Sequencing Kit. https:\/\/store.nanoporetech.com\/us\/sample-prep\/cdna-pcr-sequencing-kit.html Oxford Nanopore Technologies.  ONT. 2021. cDNA PCR Sequencing Kit. https:\/\/store.nanoporetech.com\/us\/sample-prep\/cdna-pcr-sequencing-kit.html Oxford Nanopore Technologies."},{"key":"e_1_3_2_1_36_1","unstructured":"ONT. 2021. Direct cDNA Sequencing Kit. https:\/\/store.nanoporetech.com\/us\/sample-prep\/direct-cdna-sequencing-kit.html Oxford Nanopore Technologies.  ONT. 2021. Direct cDNA Sequencing Kit. https:\/\/store.nanoporetech.com\/us\/sample-prep\/direct-cdna-sequencing-kit.html Oxford Nanopore Technologies."},{"key":"e_1_3_2_1_37_1","unstructured":"ONT. 2021. Direct RNA Sequencing Kit. https:\/\/store.nanoporetech.com\/us\/catalog\/product\/view\/id\/297\/s\/direct-rna-sequencing-kit\/category\/28\/ Oxford Nanopore Technologies.  ONT. 2021. Direct RNA Sequencing Kit. https:\/\/store.nanoporetech.com\/us\/catalog\/product\/view\/id\/297\/s\/direct-rna-sequencing-kit\/category\/28\/ Oxford Nanopore Technologies."},{"key":"e_1_3_2_1_38_1","unstructured":"ONT. 2021. MinION DNA Sequencer. https:\/\/nanoporetech.com\/products\/minion Oxford Nanopore Technologies.  ONT. 2021. MinION DNA Sequencer. https:\/\/nanoporetech.com\/products\/minion Oxford Nanopore Technologies."},{"key":"e_1_3_2_1_39_1","unstructured":"ONT. 2021. Rapid Library Preparation Kit (SQK-RAD004). https:\/\/store.nanoporetech.com\/us\/sample-prep\/rapid-sequencing-kit.html Oxford Nanopore Technologies.  ONT. 2021. Rapid Library Preparation Kit (SQK-RAD004). https:\/\/store.nanoporetech.com\/us\/sample-prep\/rapid-sequencing-kit.html Oxford Nanopore Technologies."},{"key":"e_1_3_2_1_40_1","unstructured":"ONT. 2021. Read Until API. https:\/\/github.com\/nanoporetech\/read_until_api Oxford Nanopore Technologies.  ONT. 2021. Read Until API. https:\/\/github.com\/nanoporetech\/read_until_api Oxford Nanopore Technologies."},{"key":"e_1_3_2_1_41_1","volume-title":"Optimization of primer sets and detection protocols for SARS-CoV-2 of coronavirus disease 2019 (COVID-19) using PCR and real-time PCR. Experimental & molecular medicine 52, 6","author":"Park Myungsun","year":"2020","unstructured":"Myungsun Park , Joungha Won , Byung\u00a0Yoon Choi , and C\u00a0Justin Lee . 2020. Optimization of primer sets and detection protocols for SARS-CoV-2 of coronavirus disease 2019 (COVID-19) using PCR and real-time PCR. Experimental & molecular medicine 52, 6 ( 2020 ), 963\u2013977. Myungsun Park, Joungha Won, Byung\u00a0Yoon Choi, and C\u00a0Justin Lee. 2020. Optimization of primer sets and detection protocols for SARS-CoV-2 of coronavirus disease 2019 (COVID-19) using PCR and real-time PCR. Experimental & molecular medicine 52, 6 (2020), 963\u2013977."},{"key":"e_1_3_2_1_42_1","unstructured":"Neev\u00a0V. Patel. [n. d.]. Why the CDC Botched Its Coronavirus Testing. https:\/\/www.technologyreview.com\/2020\/03\/05\/905484\/why-the-cdc-botched-its-coronavirus-testing\/ MIT Technology Review.  Neev\u00a0V. Patel. [n. d.]. Why the CDC Botched Its Coronavirus Testing. https:\/\/www.technologyreview.com\/2020\/03\/05\/905484\/why-the-cdc-botched-its-coronavirus-testing\/ MIT Technology Review."},{"key":"e_1_3_2_1_43_1","volume-title":"Nanopore adaptive sequencing for mixed samples, whole exome capture and targeted panels.BioRxiv","author":"Payne Alexander","year":"2020","unstructured":"Alexander Payne , Nadine Holmes , Thomas Clarke , Rory Munro , Bisrat Debebe , and Matthew\u00a0 W Loose . 2020. Nanopore adaptive sequencing for mixed samples, whole exome capture and targeted panels.BioRxiv ( 2020 ). Alexander Payne, Nadine Holmes, Thomas Clarke, Rory Munro, Bisrat Debebe, and Matthew\u00a0W Loose. 2020. Nanopore adaptive sequencing for mixed samples, whole exome capture and targeted panels.BioRxiv (2020)."},{"key":"e_1_3_2_1_44_1","unstructured":"Josh Quick and Nick Loman. [n. d.]. ARTIC V3 Update Notes. https:\/\/artic.network\/resources\/ncov\/ncov-amplicon-v3.pdf  Josh Quick and Nick Loman. [n. d.]. ARTIC V3 Update Notes. https:\/\/artic.network\/resources\/ncov\/ncov-amplicon-v3.pdf"},{"key":"e_1_3_2_1_45_1","unstructured":"Richard Ronan. [n. d.]. Read Until adaptive sampling. https:\/\/nanoporetech.com\/resource-centre\/read-until-adaptive-sampling Oxford Nanopore Technologies.  Richard Ronan. [n. d.]. Read Until adaptive sampling. https:\/\/nanoporetech.com\/resource-centre\/read-until-adaptive-sampling Oxford Nanopore Technologies."},{"key":"e_1_3_2_1_46_1","doi-asserted-by":"publisher","DOI":"10.1109\/ICDM.2010.21"},{"key":"e_1_3_2_1_47_1","volume-title":"Promising prospects of nanopore sequencing for algal hologenomics and structural variation discovery. BMC genomics 20, 1","author":"Sauvage Thomas","year":"2019","unstructured":"Thomas Sauvage , William\u00a0 E Schmidt , Hwan\u00a0Su Yoon , Valerie\u00a0 J Paul , and Suzanne Fredericq . 2019. Promising prospects of nanopore sequencing for algal hologenomics and structural variation discovery. BMC genomics 20, 1 ( 2019 ), 1\u201317. Thomas Sauvage, William\u00a0E Schmidt, Hwan\u00a0Su Yoon, Valerie\u00a0J Paul, and Suzanne Fredericq. 2019. Promising prospects of nanopore sequencing for algal hologenomics and structural variation discovery. BMC genomics 20, 1 (2019), 1\u201317."},{"key":"e_1_3_2_1_48_1","first-page":"1","article-title":"Dynamic time warping algorithm review. Information and Computer Science Department University of Hawaii at Manoa Honolulu","volume":"855","author":"Senin Pavel","year":"2008","unstructured":"Pavel Senin . 2008 . Dynamic time warping algorithm review. Information and Computer Science Department University of Hawaii at Manoa Honolulu , USA 855 , 1 - 23 (2008), 40. Pavel Senin. 2008. Dynamic time warping algorithm review. Information and Computer Science Department University of Hawaii at Manoa Honolulu, USA 855, 1-23 (2008), 40.","journal-title":"USA"},{"key":"e_1_3_2_1_49_1","doi-asserted-by":"publisher","DOI":"10.2807\/1560-7917.ES.2017.22.13.30494"},{"key":"e_1_3_2_1_50_1","volume-title":"De novo Identification of DNA Modifications Enabled by Genome-Guided Nanopore Signal Processing. bioRxiv","author":"Stoiber Marcus","year":"2017","unstructured":"Marcus Stoiber , Joshua Quick , Rob Egan , Ji Eun\u00a0Lee , Susan Celniker , Robert\u00a0 K. Neely , Nicholas Loman , Len\u00a0 A Pennacchio , and James Brown . 2017. De novo Identification of DNA Modifications Enabled by Genome-Guided Nanopore Signal Processing. bioRxiv ( 2017 ). https:\/\/doi.org\/10.1101\/094672 arXiv:https:\/\/www.biorxiv.org\/content\/early\/2017\/04\/10\/094672.full.pdf 10.1101\/094672 Marcus Stoiber, Joshua Quick, Rob Egan, Ji Eun\u00a0Lee, Susan Celniker, Robert\u00a0K. Neely, Nicholas Loman, Len\u00a0A Pennacchio, and James Brown. 2017. De novo Identification of DNA Modifications Enabled by Genome-Guided Nanopore Signal Processing. bioRxiv (2017). https:\/\/doi.org\/10.1101\/094672 arXiv:https:\/\/www.biorxiv.org\/content\/early\/2017\/04\/10\/094672.full.pdf"},{"key":"e_1_3_2_1_51_1","doi-asserted-by":"publisher","DOI":"10.1109\/ICPR.1992.202121"},{"key":"e_1_3_2_1_52_1","volume-title":"kmer_models. https:\/\/github.com\/nanoporetech\/kmer_models. GitHub repository","author":"Technologies Oxford\u00a0Nanopore","year":"2017","unstructured":"Oxford\u00a0Nanopore Technologies . 2017. kmer_models. https:\/\/github.com\/nanoporetech\/kmer_models. GitHub repository ( 2017 ). Oxford\u00a0Nanopore Technologies. 2017. kmer_models. https:\/\/github.com\/nanoporetech\/kmer_models. GitHub repository (2017)."},{"key":"e_1_3_2_1_53_1","unstructured":"Oxford\u00a0Nanopore Technologies. 2020. ONT Open Datasets: GM24385 Dataset Release. https:\/\/nanoporetech.github.io\/ont-open-datasets\/gm24385_2020.09\/  Oxford\u00a0Nanopore Technologies. 2020. ONT Open Datasets: GM24385 Dataset Release. https:\/\/nanoporetech.github.io\/ont-open-datasets\/gm24385_2020.09\/"},{"key":"e_1_3_2_1_54_1","doi-asserted-by":"publisher","DOI":"10.1145\/3296957.3173193"},{"key":"e_1_3_2_1_55_1","unstructured":"John\u00a0R Tyson Phillip James David Stoddart Natalie Sparks Arthur Wickenhagen Grant Hall Ji\u00a0Hyun Choi Hope Lapointe Kimia Kamelian Andrew\u00a0D Smith [n. d.]. Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanopore. bioRxiv ([n. d.]).  John\u00a0R Tyson Phillip James David Stoddart Natalie Sparks Arthur Wickenhagen Grant Hall Ji\u00a0Hyun Choi Hope Lapointe Kimia Kamelian Andrew\u00a0D Smith [n. d.]. Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanopore. bioRxiv ([n. d.])."},{"key":"e_1_3_2_1_56_1","volume-title":"Fast and accurate de novo genome assembly from long uncorrected reads. Genome research 27, 5","author":"Vaser Robert","year":"2017","unstructured":"Robert Vaser , Ivan Sovi\u0107 , Niranjan Nagarajan , and Mile \u0160iki\u0107 . 2017. Fast and accurate de novo genome assembly from long uncorrected reads. Genome research 27, 5 ( 2017 ), 737\u2013746. Robert Vaser, Ivan Sovi\u0107, Niranjan Nagarajan, and Mile \u0160iki\u0107. 2017. Fast and accurate de novo genome assembly from long uncorrected reads. Genome research 27, 5 (2017), 737\u2013746."},{"key":"e_1_3_2_1_57_1","first-page":"1649","article-title":"Rapid multiplex small DNA sequencing on the MinION nanopore sequencing platform. G3: Genes, Genomes","volume":"8","author":"Wei Shan","year":"2018","unstructured":"Shan Wei , Zachary\u00a0 R Weiss , and Zev Williams . 2018 . Rapid multiplex small DNA sequencing on the MinION nanopore sequencing platform. G3: Genes, Genomes , Genetics 8 , 5 (2018), 1649 \u2013 1657 . Shan Wei, Zachary\u00a0R Weiss, and Zev Williams. 2018. Rapid multiplex small DNA sequencing on the MinION nanopore sequencing platform. G3: Genes, Genomes, Genetics 8, 5 (2018), 1649\u20131657.","journal-title":"Genetics"},{"key":"e_1_3_2_1_58_1","volume-title":"Performance of neural network basecalling tools for Oxford Nanopore sequencing. Genome biology 20, 1","author":"Wick R","year":"2019","unstructured":"Ryan\u00a0 R Wick , Louise\u00a0 M Judd , and Kathryn\u00a0 E Holt . 2019. Performance of neural network basecalling tools for Oxford Nanopore sequencing. Genome biology 20, 1 ( 2019 ), 129. Ryan\u00a0R Wick, Louise\u00a0M Judd, and Kathryn\u00a0E Holt. 2019. Performance of neural network basecalling tools for Oxford Nanopore sequencing. Genome biology 20, 1 (2019), 129."},{"key":"e_1_3_2_1_59_1","volume-title":"Nanopore native RNA sequencing of a human poly (A) transcriptome. BioRxiv","author":"Workman E","year":"2018","unstructured":"Rachael\u00a0 E Workman , Alison\u00a0 D Tang , Paul\u00a0 S Tang , Miten Jain , John\u00a0 R Tyson , Philip\u00a0 C Zuzarte , Timothy Gilpatrick , Roham Razaghi , Joshua Quick , Norah Sadowski , 2018. Nanopore native RNA sequencing of a human poly (A) transcriptome. BioRxiv ( 2018 ), 459529. Rachael\u00a0E Workman, Alison\u00a0D Tang, Paul\u00a0S Tang, Miten Jain, John\u00a0R Tyson, Philip\u00a0C Zuzarte, Timothy Gilpatrick, Roham Razaghi, Joshua Quick, Norah Sadowski, 2018. Nanopore native RNA sequencing of a human poly (A) transcriptome. BioRxiv (2018), 459529."},{"key":"e_1_3_2_1_60_1","unstructured":"Chris Wright. 2020. Medaka. https:\/\/nanoporetech.github.io\/medaka\/ Medaka - Medaka 1.2.0 documentation.  Chris Wright. 2020. Medaka. https:\/\/nanoporetech.github.io\/medaka\/ Medaka - Medaka 1.2.0 documentation."},{"key":"e_1_3_2_1_61_1","doi-asserted-by":"publisher","DOI":"10.1109\/HPCA.2019.00044"},{"key":"e_1_3_2_1_62_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.89.13.5847"},{"key":"e_1_3_2_1_63_1","volume-title":"A pneumonia outbreak associated with a new coronavirus of probable bat origin. nature 579, 7798","author":"Zhou Peng","year":"2020","unstructured":"Peng Zhou , Xing-Lou Yang , Xian-Guang Wang , Ben Hu , Lei Zhang , Wei Zhang , Hao-Rui Si , Yan Zhu , Bei Li , Chao-Lin Huang , 2020. A pneumonia outbreak associated with a new coronavirus of probable bat origin. nature 579, 7798 ( 2020 ), 270\u2013273. Peng Zhou, Xing-Lou Yang, Xian-Guang Wang, Ben Hu, Lei Zhang, Wei Zhang, Hao-Rui Si, Yan Zhu, Bei Li, Chao-Lin Huang, 2020. A pneumonia outbreak associated with a new coronavirus of probable bat origin. nature 579, 7798 (2020), 270\u2013273."}],"event":{"name":"MICRO '21: 54th Annual IEEE\/ACM International Symposium on Microarchitecture","location":"Virtual Event Greece","acronym":"MICRO '21","sponsor":["SIGMICRO ACM Special Interest Group on Microarchitectural Research and Processing"]},"container-title":["MICRO-54: 54th Annual IEEE\/ACM International Symposium on Microarchitecture"],"original-title":[],"link":[{"URL":"https:\/\/dl.acm.org\/doi\/10.1145\/3466752.3480117","content-type":"unspecified","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/dl.acm.org\/doi\/abs\/10.1145\/3466752.3480117","content-type":"text\/html","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/dl.acm.org\/doi\/pdf\/10.1145\/3466752.3480117","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/dl.acm.org\/doi\/pdf\/10.1145\/3466752.3480117","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,17]],"date-time":"2025-06-17T20:18:57Z","timestamp":1750191537000},"score":1,"resource":{"primary":{"URL":"https:\/\/dl.acm.org\/doi\/10.1145\/3466752.3480117"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,10,17]]},"references-count":63,"alternative-id":["10.1145\/3466752.3480117","10.1145\/3466752"],"URL":"https:\/\/doi.org\/10.1145\/3466752.3480117","relation":{},"subject":[],"published":{"date-parts":[[2021,10,17]]},"assertion":[{"value":"2021-10-17","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}