{"id":"https://openalex.org/W2980639821","doi":"https://doi.org/10.1093/bioinformatics/btaa1015","title":"SneakySnake: a fast and accurate universal genome pre-alignment filter for CPUs, GPUs and FPGAs","display_name":"SneakySnake: a fast and accurate universal genome pre-alignment filter for CPUs, GPUs and FPGAs","publication_year":2020,"publication_date":"2020-11-25","ids":{"openalex":"https://openalex.org/W2980639821","doi":"https://doi.org/10.1093/bioinformatics/btaa1015","mag":"2980639821","pmid":"https://pubmed.ncbi.nlm.nih.gov/33315064"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa1015","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa1015","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/22-23/5282/36855865/btaa1015.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"preprint","indexed_in":["arxiv","crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/36/22-23/5282/36855865/btaa1015.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5081055664","display_name":"Mohammed Alser","orcid":"https://orcid.org/0000-0002-6117-3701"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Mohammed Alser","raw_affiliation_strings":["Department of Computer Science, ETH Zurich , Zurich 8006, Switzerland","Department of Information Technology and Electrical Engineering, ETH Zurich , Zurich 8006, Switzerland","Department of Computer Science, ETH Z\u00fcrich, Zurich, Switzerland"],"raw_orcid":"https://orcid.org/0000-0002-6117-3701","affiliations":[{"raw_affiliation_string":"Department of Computer Science, ETH Zurich , Zurich 8006, Switzerland","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"Department of Information Technology and Electrical Engineering, ETH Zurich , Zurich 8006, Switzerland","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"Department of Computer Science, ETH Z\u00fcrich, Zurich, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045031453","display_name":"Taha Shahroodi","orcid":"https://orcid.org/0000-0003-4576-0030"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Taha Shahroodi","raw_affiliation_strings":["Department of Computer Science, ETH Zurich , Zurich 8006, Switzerland","Department of Computer Science, ETH Z\u00fcrich, Zurich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, ETH Zurich , Zurich 8006, Switzerland","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"Department of Computer Science, ETH Z\u00fcrich, Zurich, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044416322","display_name":"Juan G\u00f3mez-Luna","orcid":"https://orcid.org/0000-0002-6514-1571"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Juan G\u00f3mez-Luna","raw_affiliation_strings":["Department of Computer Science, ETH Zurich , Zurich 8006, Switzerland","Department of Information Technology and Electrical Engineering, ETH Zurich , Zurich 8006, Switzerland","Department of Information Technology and Electrical Engineering, ETH Zurich, Zurich 8006, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, ETH Zurich , Zurich 8006, Switzerland","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"Department of Information Technology and Electrical Engineering, ETH Zurich , Zurich 8006, Switzerland","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"Department of Information Technology and Electrical Engineering, ETH Zurich, Zurich 8006, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074885623","display_name":"Can Alkan","orcid":"https://orcid.org/0000-0002-5443-0706"},"institutions":[{"id":"https://openalex.org/I168864056","display_name":"Bilkent University","ror":"https://ror.org/02vh8a032","country_code":"TR","type":"education","lineage":["https://openalex.org/I168864056"]}],"countries":["TR"],"is_corresponding":true,"raw_author_name":"Can Alkan","raw_affiliation_strings":["Department of Computer Engineering, Bilkent University , Ankara 06800, Turkey","Dept. of Comput. Eng., Bilkent Univ., Ankara, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Bilkent University , Ankara 06800, Turkey","institution_ids":["https://openalex.org/I168864056"]},{"raw_affiliation_string":"Dept. of Comput. Eng., Bilkent Univ., Ankara, Turkey","institution_ids":["https://openalex.org/I168864056"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5050695684","display_name":"Onur Mutlu","orcid":"https://orcid.org/0000-0002-0075-2312"},"institutions":[{"id":"https://openalex.org/I168864056","display_name":"Bilkent University","ror":"https://ror.org/02vh8a032","country_code":"TR","type":"education","lineage":["https://openalex.org/I168864056"]},{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]},{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["CH","TR","US"],"is_corresponding":true,"raw_author_name":"Onur Mutlu","raw_affiliation_strings":["Department of Computer Engineering, Bilkent University , Ankara 06800, Turkey","Department of Computer Science, ETH Zurich , Zurich 8006, Switzerland","Department of Electrical and Computer Engineering, Carnegie Mellon University , Pittsburgh, PA 15213, USA","Department of Information Technology and Electrical Engineering, ETH Zurich , Zurich 8006, Switzerland","Department of Computer Science, ETH Zurich, Zurich 8006, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Bilkent University , Ankara 06800, Turkey","institution_ids":["https://openalex.org/I168864056"]},{"raw_affiliation_string":"Department of Computer Science, ETH Zurich , Zurich 8006, Switzerland","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Carnegie Mellon University , Pittsburgh, PA 15213, USA","institution_ids":["https://openalex.org/I74973139"]},{"raw_affiliation_string":"Department of Information Technology and Electrical Engineering, ETH Zurich , Zurich 8006, Switzerland","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"Department of Computer Science, ETH Zurich, Zurich 8006, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5050695684","https://openalex.org/A5074885623","https://openalex.org/A5081055664"],"corresponding_institution_ids":["https://openalex.org/I168864056","https://openalex.org/I35440088","https://openalex.org/I74973139"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.8335,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.70503613,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"36","issue":"22-23","first_page":"5282","last_page":"5290"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.6158000230789185,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.6158000230789185,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12326","display_name":"Network Packet Processing and Optimization","score":0.24770000576972961,"subfield":{"id":"https://openalex.org/subfields/1708","display_name":"Hardware and Architecture"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.03290000185370445,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7658873796463013},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.6829114556312561},{"id":"https://openalex.org/keywords/field-programmable-gate-array","display_name":"Field-programmable gate array","score":0.6789872646331787},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5916568636894226},{"id":"https://openalex.org/keywords/filter","display_name":"Filter (signal processing)","score":0.5815261006355286},{"id":"https://openalex.org/keywords/path","display_name":"Path (computing)","score":0.5752906799316406},{"id":"https://openalex.org/keywords/routing","display_name":"Routing (electronic design automation)","score":0.4632021486759186},{"id":"https://openalex.org/keywords/state","display_name":"State (computer science)","score":0.43987375497817993},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3837592601776123},{"id":"https://openalex.org/keywords/computer-hardware","display_name":"Computer hardware","score":0.2935998737812042},{"id":"https://openalex.org/keywords/embedded-system","display_name":"Embedded system","score":0.24010422825813293}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7658873796463013},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.6829114556312561},{"id":"https://openalex.org/C42935608","wikidata":"https://www.wikidata.org/wiki/Q190411","display_name":"Field-programmable gate array","level":2,"score":0.6789872646331787},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5916568636894226},{"id":"https://openalex.org/C106131492","wikidata":"https://www.wikidata.org/wiki/Q3072260","display_name":"Filter (signal processing)","level":2,"score":0.5815261006355286},{"id":"https://openalex.org/C2777735758","wikidata":"https://www.wikidata.org/wiki/Q817765","display_name":"Path (computing)","level":2,"score":0.5752906799316406},{"id":"https://openalex.org/C74172769","wikidata":"https://www.wikidata.org/wiki/Q1446839","display_name":"Routing (electronic design automation)","level":2,"score":0.4632021486759186},{"id":"https://openalex.org/C48103436","wikidata":"https://www.wikidata.org/wiki/Q599031","display_name":"State (computer science)","level":2,"score":0.43987375497817993},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3837592601776123},{"id":"https://openalex.org/C9390403","wikidata":"https://www.wikidata.org/wiki/Q3966","display_name":"Computer hardware","level":1,"score":0.2935998737812042},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.24010422825813293},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.0}],"mesh":[],"locations_count":8,"locations":[{"id":"doi:10.1093/bioinformatics/btaa1015","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa1015","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/22-23/5282/36855865/btaa1015.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33315064","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33315064","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:www.research-collection.ethz.ch:20.500.11850/462178","is_oa":true,"landing_page_url":"http://hdl.handle.net/20.500.11850/462178","pdf_url":null,"source":{"id":"https://openalex.org/S4306402302","display_name":"Repository for Publications and Research Data (ETH Zurich)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I35440088","host_organization_name":"ETH Zurich","host_organization_lineage":["https://openalex.org/I35440088"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics, 36 (22-23)","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:arXiv.org:1910.09020","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1910.09020","pdf_url":"https://arxiv.org/pdf/1910.09020","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"mag:2980639821","is_oa":true,"landing_page_url":"https://arxiv.org/pdf/1910.09020v3","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"arXiv (Cornell University)","raw_type":null},{"id":"pmh:oai:zenodo.org:4537807","is_oa":true,"landing_page_url":"https://zenodo.org/record/4537807","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"info:eu-repo/semantics/other"},{"id":"doi:10.48550/arxiv.1910.09020","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.1910.09020","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"},{"id":"doi:10.3929/ethz-b-000462178","is_oa":true,"landing_page_url":"https://doi.org/10.3929/ethz-b-000462178","pdf_url":null,"source":{"id":"https://openalex.org/S7407051236","display_name":"ETH Z\u00fcrich Research Collection","issn_l":null,"issn":[],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaa1015","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa1015","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/22-23/5282/36855865/btaa1015.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306087","display_name":"Semiconductor Research Corporation","ror":"https://ror.org/047z4n946"},{"id":"https://openalex.org/F4320316785","display_name":"VMware","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2980639821.pdf","grobid_xml":"https://content.openalex.org/works/W2980639821.grobid-xml"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W1647671624","https://openalex.org/W1828154403","https://openalex.org/W1850429294","https://openalex.org/W1965942711","https://openalex.org/W1969483458","https://openalex.org/W1996065331","https://openalex.org/W2001496424","https://openalex.org/W2024873496","https://openalex.org/W2074231493","https://openalex.org/W2082346787","https://openalex.org/W2100751585","https://openalex.org/W2104549677","https://openalex.org/W2105853930","https://openalex.org/W2121716038","https://openalex.org/W2125703639","https://openalex.org/W2125831674","https://openalex.org/W2137759177","https://openalex.org/W2139747296","https://openalex.org/W2160230920","https://openalex.org/W2161014683","https://openalex.org/W2169528473","https://openalex.org/W2260037449","https://openalex.org/W2560228154","https://openalex.org/W2593716495","https://openalex.org/W2606268188","https://openalex.org/W2766489088","https://openalex.org/W2766890412","https://openalex.org/W2788876413","https://openalex.org/W2789843538","https://openalex.org/W2792035812","https://openalex.org/W2914303958","https://openalex.org/W2921796727","https://openalex.org/W2923143097","https://openalex.org/W2942400511","https://openalex.org/W2950629094","https://openalex.org/W2953174564","https://openalex.org/W2962941635","https://openalex.org/W2964007110","https://openalex.org/W2967324946","https://openalex.org/W3046494740","https://openalex.org/W3101704407","https://openalex.org/W3103269557","https://openalex.org/W6636915900","https://openalex.org/W6740813679","https://openalex.org/W6774134018"],"related_works":["https://openalex.org/W2923143097","https://openalex.org/W2813851389","https://openalex.org/W3034508728","https://openalex.org/W1972517864","https://openalex.org/W2187236549","https://openalex.org/W2080038972","https://openalex.org/W28246465","https://openalex.org/W2053908469","https://openalex.org/W2249793751","https://openalex.org/W2057496513","https://openalex.org/W32652649","https://openalex.org/W3122070438","https://openalex.org/W2126458865","https://openalex.org/W2887089575","https://openalex.org/W3131404900","https://openalex.org/W2079178546","https://openalex.org/W3206078995","https://openalex.org/W2046220835","https://openalex.org/W3013005428","https://openalex.org/W2990512463"],"abstract_inverted_index":{"MOTIVATION:":[0],"We":[1],"introduce":[2],"SneakySnake,":[3],"a":[4,69,161],"highly":[5,8],"parallel":[6],"and":[7,84,115,141,155,169,179,184,192,205,218],"accurate":[9],"pre-alignment":[10,124,137],"filter":[11],"that":[12,59,73,251],"remarkably":[13],"reduces":[14],"the":[15,30,37,48,56,64,81,86,101,121,135,198,242],"need":[16],"for":[17],"computationally":[18],"costly":[19],"sequence":[20,96,158,229],"alignment.":[21],"The":[22,76],"key":[23],"idea":[24],"of":[25,123,131,151,201,209,241,244],"SneakySnake":[26,77,108,118,146,202,225],"is":[27,98],"to":[28,36,90,110,128,134,167,182,213],"reduce":[29],"approximate":[31],"string":[32],"matching":[33],"(ASM)":[34],"problem":[35,42,83,103],"single":[38],"net":[39],"routing":[40,66],"(SNR)":[41],"in":[43,54],"VLSI":[44],"chip":[45],"layout.":[46],"In":[47],"SNR":[49,82,105],"problem,":[50],"we":[51],"are":[52,263],"interested":[53],"finding":[55],"optimal":[57,88],"path":[58,89],"connects":[60],"two":[61],"terminals":[62],"with":[63,160,175,190],"least":[65],"cost":[67],"on":[68,112,172,187,216,221],"special":[70],"grid":[71],"layout":[72],"contains":[74],"obstacles.":[75],"algorithm":[78],"quickly":[79],"solves":[80],"uses":[85],"found":[87],"decide":[91],"whether":[92],"or":[93],"not":[94,227],"performing":[95],"alignment":[97],"necessary.":[99],"Reducing":[100],"ASM":[102],"into":[104],"also":[106],"makes":[107],"efficient":[109],"implement":[111],"CPUs,":[113],"GPUs":[114],"FPGAs.":[116],"RESULTS:":[117],"significantly":[119],"improves":[120],"accuracy":[122],"filtering":[125],"by":[126,165,180,211],"up":[127,166,181,212],"four":[129],"orders":[130],"magnitude":[132],"compared":[133],"state-of-the-art":[136],"filters,":[138],"Shouji,":[139],"GateKeeper":[140],"SHD.":[142],"For":[143,195],"short":[144],"sequences,":[145,197],"accelerates":[147,203],"Edlib":[148],"(state-of-the-art":[149,157],"implementation":[150,200],"Myers's":[152],"bit-vector":[153],"algorithm)":[154],"Parasail":[156,204],"aligner":[159,208,243,254],"configurable":[162,238],"scoring":[163,239],"function),":[164],"37.7\u00d7":[168],"43.9\u00d7":[170],"(>12\u00d7":[171],"average),":[173,188,222],"respectively,":[174,189],"its":[176],"CPU":[177,199],"implementation,":[178],"413\u00d7":[183],"689\u00d7":[185],"(>400\u00d7":[186],"FPGA":[191],"GPU":[193],"acceleration.":[194],"long":[196],"KSW2":[206],"(sequence":[207],"minimap2)":[210],"979\u00d7":[214],"(276.9\u00d7":[215],"average)":[217],"91.7\u00d7":[219],"(31.7\u00d7":[220],"respectively.":[223],"As":[224],"does":[226],"replace":[228],"alignment,":[230],"users":[231],"can":[232],"still":[233],"obtain":[234],"all":[235],"capabilities":[236],"(e.g.":[237],"functions)":[240],"their":[245],"choice,":[246],"unlike":[247],"existing":[248],"acceleration":[249],"efforts":[250],"sacrifice":[252],"some":[253],"capabilities.":[255],"AVAILABILITYAND":[256],"IMPLEMENTATION:":[257],"https://github.com/CMU-SAFARI/SneakySnake.":[258],"SUPPLEMENTARY":[259],"INFORMATION:":[260],"Supplementary":[261],"data":[262],"available":[264],"at":[265],"Bioinformatics":[266],"online.":[267]},"counts_by_year":[{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}