{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,8]],"date-time":"2024-09-08T15:42:55Z","timestamp":1725810175001},"reference-count":276,"publisher":"IEEE","license":[{"start":{"date-parts":[[2024,6,29]],"date-time":"2024-06-29T00:00:00Z","timestamp":1719619200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2024,6,29]],"date-time":"2024-06-29T00:00:00Z","timestamp":1719619200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000028","name":"Semiconductor Research Corporation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000028","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,6,29]]},"DOI":"10.1109\/isca59077.2024.00054","type":"proceedings-article","created":{"date-parts":[[2024,8,1]],"date-time":"2024-08-01T17:38:44Z","timestamp":1722533924000},"page":"660-677","source":"Crossref","is-referenced-by-count":0,"title":["MegIS: High-Performance, Energy-Efficient, and Low-Cost Metagenomic Analysis with In-Storage Processing"],"prefix":"10.1109","author":[{"given":"Nika Mansouri","family":"Ghiasi","sequence":"first","affiliation":[{"name":"ETH Zürich"}]},{"given":"Mohammad","family":"Sadrosadati","sequence":"additional","affiliation":[{"name":"ETH Zürich"}]},{"given":"Harun","family":"Mustafa","sequence":"additional","affiliation":[{"name":"ETH Zürich"}]},{"given":"Arvid","family":"Gollwitzer","sequence":"additional","affiliation":[{"name":"ETH Zürich"}]},{"given":"Can","family":"Firtina","sequence":"additional","affiliation":[{"name":"ETH Zürich"}]},{"given":"Julien","family":"Eudine","sequence":"additional","affiliation":[{"name":"ETH Zürich"}]},{"given":"Haiyu","family":"Mao","sequence":"additional","affiliation":[{"name":"ETH Zürich"}]},{"given":"Jo\u00ebl","family":"Lindegger","sequence":"additional","affiliation":[{"name":"ETH Zürich"}]},{"given":"Meryem Banu","family":"Cavlak","sequence":"additional","affiliation":[{"name":"ETH Zürich"}]},{"given":"Mohammed","family":"Alser","sequence":"additional","affiliation":[{"name":"ETH Zürich"}]},{"given":"Jisung","family":"Park","sequence":"additional","affiliation":[{"name":"POSTECH"}]},{"given":"Onur","family":"Mutlu","sequence":"additional","affiliation":[{"name":"ETH Zürich"}]}],"member":"263","reference":[{"key":"ref1","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4419-7089-3_15"},{"key":"ref2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1261359"},{"key":"ref3","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro.2017.87"},{"key":"ref4","doi-asserted-by":"publisher","DOI":"10.1109\/MICRO50266.2020.00081"},{"key":"ref5","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty191"},{"key":"ref6","doi-asserted-by":"publisher","DOI":"10.1109\/ISCA45697.2020.00031"},{"key":"ref7","doi-asserted-by":"publisher","DOI":"10.1145\/3296957.3173193"},{"key":"ref8","doi-asserted-by":"publisher","DOI":"10.1109\/ISLPED.2019.8824830"},{"key":"ref9","doi-asserted-by":"publisher","DOI":"10.1016\/j.tips.2016.10.001"},{"key":"ref10","doi-asserted-by":"publisher","DOI":"10.1007\/s00345-019-02731-9"},{"key":"ref11","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-020-64616-x"},{"key":"ref12","doi-asserted-by":"publisher","DOI":"10.1016\/j.cels.2015.07.006"},{"key":"ref13","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.00018-16"},{"key":"ref14","doi-asserted-by":"publisher","DOI":"10.3390\/cimb43020061"},{"key":"ref15","doi-asserted-by":"publisher","DOI":"10.1128\/Spectrum.00197-21"},{"key":"ref16","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2017.00230"},{"key":"ref17","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty407"},{"key":"ref18","doi-asserted-by":"publisher","DOI":"10.1038\/s41576-022-00551-z"},{"key":"ref19","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jiz151"},{"key":"ref20","doi-asserted-by":"publisher","DOI":"10.1038\/s41576-019-0113-7"},{"key":"ref21","doi-asserted-by":"publisher","DOI":"10.1016\/j.csbj.2020.11.049"},{"key":"ref22","doi-asserted-by":"publisher","DOI":"10.1016\/j.humimm.2021.02.012"},{"key":"ref23","doi-asserted-by":"publisher","DOI":"10.1109\/MM.2020.3013728"},{"key":"ref24","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkab1053"},{"volume-title":"European Nucleotide Archive Statistics","year":"2023","key":"ref25"},{"key":"ref26","doi-asserted-by":"publisher","DOI":"10.1016\/j.csbj.2022.08.019"},{"key":"ref27","article-title":"International Nucleotide Sequence Database Collaboration","author":"Leinonen","year":"2010","journal-title":"The Sequence Read Archive. Nucleic Acids Research"},{"key":"ref28","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-024-03181-2"},{"key":"ref29","doi-asserted-by":"publisher","DOI":"10.1016\/j.ailsci.2021.100011"},{"key":"ref30","doi-asserted-by":"publisher","DOI":"10.1145\/3410463.3414626"},{"key":"ref31","doi-asserted-by":"publisher","DOI":"10.1145\/3613424.3614252"},{"key":"ref32","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btad352"},{"key":"ref33","article-title":"Targetcall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling Filtering","author":"Cavlak","year":"2023","journal-title":"APBC"},{"key":"ref34","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkac1032"},{"key":"ref35","article-title":"Metagraph: Indexing and Analysing Nucleotide Archives at Petabase-scale","author":"Karasikov","year":"2020","journal-title":"bioRxiv"},{"key":"ref36","article-title":"Indexing and searching petabyte-scale nucleotide resources","author":"Shiryev","year":"2023","journal-title":"bioRxiv"},{"volume-title":"Introducing pebblescout: Index and search petabyte-scale sequence resources faster than ever","year":"2023","key":"ref37"},{"key":"ref38","doi-asserted-by":"publisher","DOI":"10.1038\/s43588-024-00596-6"},{"key":"ref39","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btad225"},{"volume-title":"Re-evaluating the blast nucleotide database (nt)","year":"2022","key":"ref40"},{"key":"ref41","doi-asserted-by":"publisher","DOI":"10.1016\/j.tig.2010.05.003"},{"key":"ref42","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-018-1554-6"},{"key":"ref43","article-title":"Reference Sequence (RefSeq) Database at NCBI: Current Status, Taxonomic Expansion, and Functional Annotation","author":"Nuala","year":"2016","journal-title":"Nucleic Acids Research"},{"key":"ref44","doi-asserted-by":"publisher","DOI":"10.1093\/nsr\/nwaa280"},{"key":"ref45","doi-asserted-by":"publisher","DOI":"10.1007\/978-981-99-5720-0_11"},{"key":"ref46","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-023-01662-6"},{"key":"ref47","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-022-05325-5"},{"key":"ref48","doi-asserted-by":"publisher","DOI":"10.1101\/gr.210641.116"},{"key":"ref49","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1891-0"},{"key":"ref50","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btx520"},{"key":"ref51","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-024-03244-4"},{"key":"ref52","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-10934-2"},{"key":"ref53","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-021-04089-5"},{"key":"ref54","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-08844-4"},{"key":"ref55","doi-asserted-by":"publisher","DOI":"10.1212\/NXI.0000000000000251"},{"key":"ref56","doi-asserted-by":"publisher","DOI":"10.1128\/mbio.01607-23"},{"key":"ref57","doi-asserted-by":"publisher","DOI":"10.21105\/joss.04908"},{"key":"ref58","doi-asserted-by":"publisher","DOI":"10.1016\/j.cels.2015.07.008"},{"key":"ref59","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-022-01431-4"},{"key":"ref60","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-021-02443-7"},{"key":"ref61","doi-asserted-by":"publisher","DOI":"10.1145\/3613424.3614262"},{"key":"ref62","doi-asserted-by":"publisher","DOI":"10.1145\/3472456.3472460"},{"key":"ref63","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbad092"},{"key":"ref64","doi-asserted-by":"publisher","DOI":"10.1109\/ISCA52012.2021.00028"},{"key":"ref65","doi-asserted-by":"publisher","DOI":"10.1145\/3470496.3527424"},{"key":"ref66","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-016-1434-6"},{"key":"ref67","doi-asserted-by":"publisher","DOI":"10.1145\/3524059.3532367"},{"key":"ref68","doi-asserted-by":"publisher","DOI":"10.1109\/ACCESS.2022.3195878"},{"key":"ref69","doi-asserted-by":"publisher","DOI":"10.1128\/msystems.01378-21"},{"key":"ref70","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0025353"},{"key":"ref71","doi-asserted-by":"publisher","DOI":"10.1109\/JPROC.2017.2713127"},{"key":"ref72","doi-asserted-by":"publisher","DOI":"10.1007\/978-981-13-0599-3_9"},{"key":"ref73","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2014-15-3-r46"},{"key":"ref74","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3589"},{"key":"ref75","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-015-1419-2"},{"key":"ref76","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btw150"},{"key":"ref77","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btaa458"},{"key":"ref78","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-020-02014-2"},{"key":"ref79","doi-asserted-by":"publisher","DOI":"10.1145\/3579371.3589071"},{"key":"ref80","doi-asserted-by":"publisher","DOI":"10.1109\/ISCA.2018.00041"},{"key":"ref81","doi-asserted-by":"publisher","DOI":"10.1109\/MICRO56248.2022.00038"},{"key":"ref82","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-020-02159-0"},{"key":"ref83","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btac845"},{"volume-title":"Samsung SSD PM1735","year":"2020","key":"ref84"},{"volume-title":"Samsung SSD 870 EVO","year":"2021","key":"ref85"},{"volume-title":"Cortex-R4","year":"2011","key":"ref86"},{"volume-title":"Samsung SSD 860 PRO","year":"2018","key":"ref87"},{"key":"ref88","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-021-01141-3"},{"key":"ref89","doi-asserted-by":"publisher","DOI":"10.7717\/peerj-cs.104"},{"key":"ref90","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.00020-16"},{"key":"ref91","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1010493"},{"key":"ref92","doi-asserted-by":"publisher","DOI":"10.1109\/ICCD.2013.6657034"},{"key":"ref93","doi-asserted-by":"publisher","DOI":"10.1109\/tcsi.2010.2071990"},{"key":"ref94","article-title":"LDPC-in-SSD: Making Advanced Error Correction Codes Work Effectively in Solid State Drives","author":"Zhao","year":"2013","journal-title":"In FAST"},{"key":"ref95","doi-asserted-by":"publisher","DOI":"10.1016\/S0019-9958(60)90287-4"},{"key":"ref96","doi-asserted-by":"publisher","DOI":"10.1109\/JSAC.2014.140508"},{"key":"ref97","doi-asserted-by":"publisher","DOI":"10.1109\/HPCA.2017.61"},{"key":"ref98","doi-asserted-by":"publisher","DOI":"10.1145\/3224432"},{"key":"ref99","doi-asserted-by":"publisher","DOI":"10.1109\/HPCA.2018.00050"},{"key":"ref100","doi-asserted-by":"publisher","DOI":"10.1109\/DSN.2015.49"},{"key":"ref101","article-title":"Error Analysis and Management for MLC NAND Flash Memory","author":"Cai","year":"2013","journal-title":"Intel Technology"},{"key":"ref102","doi-asserted-by":"publisher","DOI":"10.1109\/ICCD.2012.6378623"},{"key":"ref103","doi-asserted-by":"publisher","DOI":"10.1109\/tcad.2015.2504868"},{"key":"ref104","doi-asserted-by":"publisher","DOI":"10.1109\/MSST.2015.7208284"},{"key":"ref105","doi-asserted-by":"publisher","DOI":"10.1109\/MICRO56248.2022.00035"},{"key":"ref106","doi-asserted-by":"publisher","DOI":"10.1145\/3579371.3589093"},{"key":"ref107","doi-asserted-by":"publisher","DOI":"10.1145\/3352460.3358320"},{"key":"ref108","doi-asserted-by":"publisher","DOI":"10.1145\/3466752.3480108"},{"key":"ref109","doi-asserted-by":"publisher","DOI":"10.1145\/3123939.3124553"},{"key":"ref110","article-title":"GenStore: A High-Performance in-Storage Processing System for Genome Sequence Analysis","author":"Ghiasi","year":"2022","journal-title":"In ASPLOS"},{"key":"ref111","doi-asserted-by":"publisher","DOI":"10.1109\/HPCA57654.2024.00033"},{"key":"ref112","doi-asserted-by":"publisher","DOI":"10.1109\/HPCA57654.2024.00034"},{"key":"ref113","doi-asserted-by":"publisher","DOI":"10.1109\/HPCA56546.2023.10071024"},{"key":"ref114","article-title":"GLIST: Towards In-Storage Graph Learning","author":"Li","year":"2021","journal-title":"In ATC"},{"volume-title":"New Enterprise SSD Controllers","key":"ref115"},{"key":"ref116","doi-asserted-by":"publisher","DOI":"10.1145\/3579371.3589096"},{"key":"ref117","doi-asserted-by":"publisher","DOI":"10.1145\/2628071.2628098"},{"key":"ref118","doi-asserted-by":"publisher","DOI":"10.1145\/3373376.3378490"},{"key":"ref119","doi-asserted-by":"publisher","DOI":"10.1145\/2897937.2898032"},{"key":"ref120","article-title":"RansomeBlocker: a Low-Overhead Ransomware-Proof SSD","author":"Park","year":"2019","journal-title":"In DAC"},{"key":"ref121","doi-asserted-by":"publisher","DOI":"10.1145\/1244002.1244248"},{"key":"ref122","article-title":"Cognitive SSD: A Deep Learning Engine for In-Storage Data Retrieval","author":"Liang","year":"2019","journal-title":"In ATC"},{"key":"ref123","doi-asserted-by":"publisher","DOI":"10.1145\/3409963.3410501"},{"key":"ref124","doi-asserted-by":"publisher","DOI":"10.1109\/ICCE-Asia53811.2021.9641965"},{"key":"ref125","article-title":"SSD in-storage computing for list intersection","author":"JianguoWang","year":"2016","journal-title":"In DaMoN"},{"key":"ref126","doi-asserted-by":"publisher","DOI":"10.3389\/fnins.2020.571292"},{"key":"ref127","doi-asserted-by":"publisher","DOI":"10.1109\/TC.2021.3082003"},{"key":"ref128","doi-asserted-by":"publisher","DOI":"10.1002\/aisy.202000161"},{"key":"ref129","doi-asserted-by":"publisher","DOI":"10.1109\/EDTM53872.2022.9797982"},{"key":"ref130","article-title":"Three-dimensional NAND flash for vector\u2013matrix multiplication","author":"PanniWang","year":"2018","journal-title":"In VLSI"},{"key":"ref131","doi-asserted-by":"publisher","DOI":"10.1109\/TCSI.2018.2885574"},{"key":"ref132","doi-asserted-by":"publisher","DOI":"10.1109\/ISCAS45731.2020.9180920"},{"key":"ref133","doi-asserted-by":"publisher","DOI":"10.1145\/3310149"},{"key":"ref134","doi-asserted-by":"publisher","DOI":"10.1109\/ISCA.2018.00042"},{"key":"ref135","doi-asserted-by":"publisher","DOI":"10.1145\/2463676.2465295"},{"key":"ref136","article-title":"Willow: A User-Programmable SSD","author":"Seshadri","year":"2014","journal-title":"In OSDI"},{"key":"ref137","doi-asserted-by":"publisher","DOI":"10.1016\/j.ins.2015.07.056"},{"key":"ref138","doi-asserted-by":"publisher","DOI":"10.1109\/2.928624"},{"key":"ref139","article-title":"Active Storage for Large-Scale Data Mining and Multimedia Applications","author":"Riedel","year":"1998","journal-title":"In VLDB"},{"key":"ref140","doi-asserted-by":"publisher","DOI":"10.1145\/3470496.3527391"},{"key":"ref141","article-title":"REACT: Scalable and High-performance Regular Expression Pattern Matching Accelerator for In-storage Processing","author":"Jeong","year":"2019","journal-title":"TPDS"},{"key":"ref142","doi-asserted-by":"publisher","DOI":"10.1109\/HPEC.2016.7761588"},{"key":"ref143","doi-asserted-by":"publisher","DOI":"10.1145\/3007787.3001154"},{"key":"ref144","article-title":"Enabling Costeffective Data Processing with Smart SSD","author":"Kang","year":"2013","journal-title":"In MSST"},{"key":"ref145","doi-asserted-by":"publisher","DOI":"10.1145\/3302424.3303983"},{"key":"ref146","doi-asserted-by":"publisher","DOI":"10.1145\/291069.291026"},{"key":"ref147","doi-asserted-by":"publisher","DOI":"10.1145\/290593.290602"},{"key":"ref148","doi-asserted-by":"publisher","DOI":"10.1109\/tnnls.2017.2778940"},{"key":"ref149","article-title":"Active flash: Towards energy-efficient, in-situ data analytics on extreme-scale machines","author":"Tiwari","year":"2013","journal-title":"In FAST"},{"key":"ref150","article-title":"Reducing data movement costs using energyefficient, active computation on ssd","author":"Tiwari","year":"2012","journal-title":"In HotPower"},{"key":"ref151","doi-asserted-by":"publisher","DOI":"10.1109\/MSST.2012.6232366"},{"key":"ref152","doi-asserted-by":"publisher","DOI":"10.1145\/2505515.2507847"},{"key":"ref153","doi-asserted-by":"publisher","DOI":"10.1109\/IPDPSW.2018.00195"},{"key":"ref154","doi-asserted-by":"publisher","DOI":"10.1145\/3466752.3480109"},{"key":"ref155","doi-asserted-by":"publisher","DOI":"10.1145\/3466752.3480078"},{"key":"ref156","doi-asserted-by":"publisher","DOI":"10.1109\/MICRO56248.2022.00069"},{"key":"ref157","doi-asserted-by":"publisher","DOI":"10.1145\/2872887.2750412"},{"key":"ref158","doi-asserted-by":"publisher","DOI":"10.1145\/2898996"},{"key":"ref159","doi-asserted-by":"publisher","DOI":"10.1109\/EMPDP.2019.8671589"},{"key":"ref160","doi-asserted-by":"publisher","DOI":"10.1109\/LCA.2020.3009347"},{"key":"ref161","article-title":"CIDR: A Cost-effective In-line Data Reduction System for Terabit-persecond Scale SSD Arrays","author":"Ajdari","year":"2019","journal-title":"In HPCA"},{"key":"ref162","article-title":"XSD: Accelerating Mapreduce by Harnessing the GPU inside an SSD","author":"Cho","year":"2013","journal-title":"In WoNDP"},{"journal-title":"Why Metagenomics? In The New Science of Metagenomics: Revealing the Secrets of our Microbial Planet","year":"2007","key":"ref163"},{"volume-title":"Using the Latest Technology to Detect Outbreaks and Protect the Public\u2019s Health","year":"2020","key":"ref164"},{"key":"ref165","doi-asserted-by":"publisher","DOI":"10.1093\/ofid\/ofad500.1603"},{"volume-title":"AMD: Developing Faster Tests","year":"2019","key":"ref166"},{"key":"ref167","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.1002195"},{"key":"ref168","doi-asserted-by":"publisher","DOI":"10.1038\/nature.2015.17912"},{"key":"ref169","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-021-04332-2"},{"key":"ref170","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-022-01539-7"},{"key":"ref171","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-021-01108-x"},{"key":"ref172","doi-asserted-by":"publisher","DOI":"10.1080\/14737159.2021.2001329"},{"volume-title":"NovaSeq X Series Specifications","year":"2023","key":"ref173"},{"key":"ref174","doi-asserted-by":"publisher","DOI":"10.1038\/srep09687"},{"key":"ref175","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btab264"},{"key":"ref176","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btad272"},{"key":"ref177","article-title":"Targeted Nanopore Sequencing by Real-time Mapping of Raw Electrical Signal with UNCALLED","author":"Kovaka","year":"2020","journal-title":"Nature Biotechnology"},{"key":"ref178","doi-asserted-by":"publisher","DOI":"10.1109\/DAC56929.2023.10247887"},{"key":"ref179","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-020-00746-x"},{"key":"ref180","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-021-02511-y"},{"key":"ref181","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btac223"},{"volume-title":"NovaSeq 6000 System Specifications","year":"2020","key":"ref182"},{"key":"ref183","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-016-1103-0"},{"key":"ref184","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giy033"},{"key":"ref185","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkp967"},{"volume-title":"AMD\u00ae EPYC\u00ae 7742 CPU","key":"ref186"},{"journal-title":"4Gb: x4, x8, x16 DDR4 SDRAM Data Sheet","year":"2016","key":"ref187"},{"volume-title":"SATA revision 3.0 specifications","key":"ref188"},{"volume-title":"PCI Express Base Specification Revision 4.0, Version 1.0","key":"ref189"},{"volume-title":"Samsung PM1735","key":"ref190"},{"volume-title":"Samsung PM9A3","key":"ref191"},{"volume-title":"Samsung 870 EVO","key":"ref192"},{"volume-title":"Centrifuge","year":"2020","author":"Kim","key":"ref193"},{"key":"ref194","doi-asserted-by":"publisher","DOI":"10.1093\/bioadv\/vbac029"},{"key":"ref195","article-title":"Themisto: a scalable colored k-mer index for sensitive pseudoalignment against hundreds of thousands of bacterial genomes","author":"JarnoNAlanko","year":"2023","journal-title":"Bioinformatics"},{"key":"ref196","doi-asserted-by":"publisher","DOI":"10.1186\/s13015-024-00251-9"},{"key":"ref197","doi-asserted-by":"publisher","DOI":"10.1145\/3470496.3527422"},{"key":"ref198","doi-asserted-by":"publisher","DOI":"10.1007\/978-981-16-7487-7_7"},{"key":"ref199","doi-asserted-by":"publisher","DOI":"10.1147\/JRD.2019.2934048"},{"key":"ref200","doi-asserted-by":"publisher","DOI":"10.1016\/j.micpro.2019.01.009"},{"key":"ref201","article-title":"Enabling the Adoption of Processing-in-memory: Challenges, Mechanisms, Future Research Directions","author":"Ghose","year":"2018","journal-title":"arXiv"},{"key":"ref202","article-title":"MegIS: A High-Performance, Energy-Efficient, and Low-Cost In-Storage Processing System for Metagenomic Analysis","author":"Ghiasi","year":"2024","journal-title":"arXiv"},{"key":"ref203","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btx304"},{"key":"ref204","doi-asserted-by":"publisher","DOI":"10.1109\/ISCA45697.2020.00033"},{"key":"ref205","doi-asserted-by":"publisher","DOI":"10.1109\/FCCM53951.2022.9786209"},{"key":"ref206","doi-asserted-by":"publisher","DOI":"10.1109\/icfpt56656.2022.9974209"},{"key":"ref207","doi-asserted-by":"publisher","DOI":"10.7717\/peerj-cs.94"},{"key":"ref208","doi-asserted-by":"publisher","DOI":"10.21105\/joss.00505"},{"volume-title":"Samsung SSD 980 PRO","year":"2020","key":"ref209"},{"key":"ref210","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btac237"},{"key":"ref211","doi-asserted-by":"publisher","DOI":"10.1101\/gr.260604.119"},{"key":"ref212","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkab200"},{"key":"ref213","article-title":"Gen-Cache: Leveraging In-cache Operators for Efficient Sequence Alignment","author":"Nag","year":"2019","journal-title":"In MICRO"},{"key":"ref214","doi-asserted-by":"publisher","DOI":"10.1109\/ISCA.2018.00017"},{"key":"ref215","doi-asserted-by":"publisher","DOI":"10.1145\/3061639.3062264"},{"key":"ref216","article-title":"A flash-memory based file system","author":"Kawaguchi","year":"1995","journal-title":"In ATC"},{"volume-title":"Product Flyer: Micron 3D NAND Flash Memory","year":"2016","key":"ref217"},{"volume-title":"Design Compiler","key":"ref218"},{"journal-title":"UMK65LSCLLMVBBL_A-UMC 65 nm Low-K 1.2V\/1.0V Low Leakage LVT Tapless Standard Cell Library, version A02","year":"2008","key":"ref219"},{"volume-title":"Innovus Implementation System","key":"ref220"},{"key":"ref221","doi-asserted-by":"publisher","DOI":"10.1109\/lca.2015.2414456"},{"volume-title":"Ramulator Source Code","author":"Kim","key":"ref222"},{"key":"ref223","article-title":"MQSim: A Framework for Enabling Realistic Studies of Modern Multi-queue SSD Devices","author":"Tavakkol","year":"2018","journal-title":"In FAST"},{"volume-title":"MQSim Source Code","author":"Tavakkol","key":"ref224"},{"volume-title":"LPDDR4","key":"ref225"},{"key":"ref226","doi-asserted-by":"publisher","DOI":"10.1145\/3366708"},{"volume-title":"AMD\u00ae \u03bcProf","year":"2021","key":"ref227"},{"key":"ref228","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4458"},{"volume-title":"MinION Mk1B IT Requirements","year":"2021","key":"ref229"},{"key":"ref230","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bby017"},{"key":"ref231","doi-asserted-by":"publisher","DOI":"10.1016\/j.vlsi.2017.02.002"},{"key":"ref232","doi-asserted-by":"publisher","DOI":"10.1186\/1752-0509-6-S1-S16"},{"key":"ref233","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btt736"},{"key":"ref234","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-014-0406-y"},{"key":"ref235","doi-asserted-by":"publisher","DOI":"10.1109\/ACCESS.2020.3003918"},{"key":"ref236","doi-asserted-by":"publisher","DOI":"10.1109\/BioCAS58349.2023.10388531"},{"key":"ref237","doi-asserted-by":"publisher","DOI":"10.1007\/978-981-16-2380-6_49"},{"key":"ref238","doi-asserted-by":"publisher","DOI":"10.1145\/3466752.3480117"},{"key":"ref239","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giad046"},{"key":"ref240","doi-asserted-by":"publisher","DOI":"10.1016\/j.isci.2021.102696"},{"key":"ref241","doi-asserted-by":"publisher","DOI":"10.1145\/3195970.3196098"},{"key":"ref242","article-title":"GeNVoM: Read Mapping Near Non-Volatile Memory","author":"Karen Khatamifard","year":"2021","journal-title":"TCBB"},{"key":"ref243","doi-asserted-by":"publisher","DOI":"10.1007\/s11390-020-0825-3"},{"key":"ref244","doi-asserted-by":"publisher","DOI":"10.1145\/3316781.3317764"},{"key":"ref245","doi-asserted-by":"publisher","DOI":"10.1109\/LCA.2018.2854700"},{"key":"ref246","doi-asserted-by":"publisher","DOI":"10.1109\/ISCA.2014.6853226"},{"key":"ref247","article-title":"Bitmapper2: A GPU-accelerated Allmapper Based on The Sparse Q-gram Index","author":"Cheng","year":"2018","journal-title":"TCBB"},{"key":"ref248","doi-asserted-by":"publisher","DOI":"10.1016\/j.compbiolchem.2018.03.024"},{"key":"ref249","doi-asserted-by":"publisher","DOI":"10.1145\/3039902.3039910"},{"key":"ref250","doi-asserted-by":"publisher","DOI":"10.1109\/ipdps47924.2020.00055"},{"key":"ref251","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-019-3086-9"},{"key":"ref252","doi-asserted-by":"publisher","DOI":"10.1109\/IPDPSW.2017.75"},{"key":"ref253","doi-asserted-by":"publisher","DOI":"10.1109\/TPDS.2016.2515597"},{"key":"ref254","doi-asserted-by":"publisher","DOI":"10.1002\/cpe.3371"},{"key":"ref255","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-14-117"},{"key":"ref256","doi-asserted-by":"publisher","DOI":"10.1186\/1756-0500-2-73"},{"key":"ref257","doi-asserted-by":"publisher","DOI":"10.1186\/1756-0500-3-93"},{"key":"ref258","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.808"},{"key":"ref259","doi-asserted-by":"publisher","DOI":"10.4236\/ojgen.2017.71002"},{"key":"ref260","doi-asserted-by":"publisher","DOI":"10.1109\/FCCM.2016.18"},{"key":"ref261","doi-asserted-by":"publisher","DOI":"10.1109\/TCBB.2014.2326876"},{"key":"ref262","doi-asserted-by":"publisher","DOI":"10.1109\/TPDS.2021.3051011"},{"key":"ref263","doi-asserted-by":"publisher","DOI":"10.1109\/MICRO50266.2020.00080"},{"key":"ref264","article-title":"ASAP: Accelerated Shortread Alignment on Programmable Hardware","author":"Banerjee","year":"2019","journal-title":"TC"},{"key":"ref265","doi-asserted-by":"publisher","DOI":"10.1007\/s12539-017-0225-8"},{"key":"ref266","doi-asserted-by":"publisher","DOI":"10.1109\/tpds.2015.2444376"},{"key":"ref267","doi-asserted-by":"publisher","DOI":"10.1109\/FCCM.2015.27"},{"key":"ref268","doi-asserted-by":"publisher","DOI":"10.1186\/s12918-018-0614-6"},{"key":"ref269","doi-asserted-by":"publisher","DOI":"10.1109\/FPL53798.2021.00033"},{"key":"ref270","doi-asserted-by":"publisher","DOI":"10.1109\/ISVLSI51109.2021.00042"},{"key":"ref271","doi-asserted-by":"publisher","DOI":"10.1109\/MM.2021.3072385"},{"key":"ref272","doi-asserted-by":"publisher","DOI":"10.1109\/HPCA.2019.00044"},{"key":"ref273","doi-asserted-by":"publisher","DOI":"10.14778\/3421424.3421425"},{"key":"ref274","doi-asserted-by":"publisher","DOI":"10.1109\/ISCA52012.2021.00038"},{"key":"ref275","doi-asserted-by":"publisher","DOI":"10.1109\/FPL.2019.00035"},{"key":"ref276","doi-asserted-by":"publisher","DOI":"10.1145\/3632952"}],"event":{"name":"2024 ACM\/IEEE 51st Annual International Symposium on Computer Architecture (ISCA)","start":{"date-parts":[[2024,6,29]]},"location":"Buenos Aires, Argentina","end":{"date-parts":[[2024,7,3]]}},"container-title":["2024 ACM\/IEEE 51st Annual International Symposium on Computer Architecture (ISCA)"],"original-title":[],"link":[{"URL":"http:\/\/xplorestaging.ieee.org\/ielx8\/10609566\/10609567\/10609570.pdf?arnumber=10609570","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,8,3]],"date-time":"2024-08-03T05:25:24Z","timestamp":1722662724000},"score":1,"resource":{"primary":{"URL":"https:\/\/ieeexplore.ieee.org\/document\/10609570\/"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,6,29]]},"references-count":276,"URL":"https:\/\/doi.org\/10.1109\/isca59077.2024.00054","relation":{},"subject":[],"published":{"date-parts":[[2024,6,29]]}}}