{"id":"https://openalex.org/W7131662308","doi":"https://doi.org/10.1093/bioinformatics/btag087","title":"Rawsamble: overlapping raw nanopore signals using a hash-based seeding mechanism","display_name":"Rawsamble: overlapping raw nanopore signals using a hash-based seeding mechanism","publication_year":2026,"publication_date":"2026-02-25","ids":{"openalex":"https://openalex.org/W7131662308","doi":"https://doi.org/10.1093/bioinformatics/btag087","pmid":"https://pubmed.ncbi.nlm.nih.gov/41746292"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btag087","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag087","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bioinformatics/btag087","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5066286509","display_name":"Can F\u0131rt\u0131na","orcid":"https://orcid.org/0000-0002-6548-7863"},"institutions":[{"id":"https://openalex.org/I126744593","display_name":"University of Maryland, Baltimore","ror":"https://ror.org/04rq5mt64","country_code":"US","type":"education","lineage":["https://openalex.org/I126744593"]},{"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/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["CH","US"],"is_corresponding":false,"raw_author_name":"Can Firtina","raw_affiliation_strings":["Department of Computer Science, University of Maryland , MD 20742,","Department of Information Technology and Electrical Engineering, ETH Zurich , Zurich, 8092,"],"raw_orcid":"https://orcid.org/0000-0002-6548-7863","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Maryland , MD 20742,","institution_ids":["https://openalex.org/I66946132","https://openalex.org/I126744593"]},{"raw_affiliation_string":"Department of Information Technology and Electrical Engineering, ETH Zurich , Zurich, 8092,","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061438573","display_name":"Maximilian Mordig","orcid":"https://orcid.org/0000-0002-5731-484X"},"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"]},{"id":"https://openalex.org/I4210135521","display_name":"Max Planck Institute for Intelligent Systems","ror":"https://ror.org/04fq9j139","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210135521"]}],"countries":["CH","DE"],"is_corresponding":false,"raw_author_name":"Maximilian Mordig","raw_affiliation_strings":["Department of Computer Science, ETH Zurich , Zurich, 8092,","Max Planck Institute for Intelligent Systems , Tubingen, 72076,"],"raw_orcid":"https://orcid.org/0000-0002-5731-484X","affiliations":[{"raw_affiliation_string":"Department of Computer Science, ETH Zurich , Zurich, 8092,","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"Max Planck Institute for Intelligent Systems , Tubingen, 72076,","institution_ids":["https://openalex.org/I4210135521"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033347097","display_name":"Harun Mustafa","orcid":"https://orcid.org/0000-0002-2125-6086"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"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/I4210100468","display_name":"University Hospital of Zurich","ror":"https://ror.org/01462r250","country_code":"CH","type":"funder","lineage":["https://openalex.org/I4210100468"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Harun Mustafa","raw_affiliation_strings":["Department of Computer Science, ETH Zurich , Zurich, 8092,","Swiss Institute of Bioinformatics , Zurich, 8057,","University Hospital Zurich , Zurich, 8091,"],"raw_orcid":"https://orcid.org/0000-0002-2125-6086","affiliations":[{"raw_affiliation_string":"Department of Computer Science, ETH Zurich , Zurich, 8092,","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"Swiss Institute of Bioinformatics , Zurich, 8057,","institution_ids":["https://openalex.org/I12708293"]},{"raw_affiliation_string":"University Hospital Zurich , Zurich, 8091,","institution_ids":["https://openalex.org/I4210100468"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5126942599","display_name":"Sayan Goswami","orcid":null},"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":"Sayan Goswami","raw_affiliation_strings":["Department of Computer Science, ETH Zurich , Zurich, 8092,"],"raw_orcid":"https://orcid.org/0000-0002-7519-524X","affiliations":[{"raw_affiliation_string":"Department of Computer Science, ETH Zurich , Zurich, 8092,","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048764555","display_name":"Nika Mansouri Ghiasi","orcid":"https://orcid.org/0000-0002-0833-0042"},"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":"Nika Mansouri Ghiasi","raw_affiliation_strings":["Department of Information Technology and Electrical Engineering, ETH Zurich , Zurich, 8092,"],"raw_orcid":"https://orcid.org/0000-0002-0833-0042","affiliations":[{"raw_affiliation_string":"Department of Information Technology and Electrical Engineering, ETH Zurich , Zurich, 8092,","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115038003","display_name":"Stefano Mercogliano","orcid":null},"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":"Stefano Mercogliano","raw_affiliation_strings":["Department of Information Technology and Electrical Engineering, ETH Zurich , Zurich, 8092,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Information Technology and Electrical Engineering, ETH Zurich , Zurich, 8092,","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115038004","display_name":"Furkan Eris","orcid":"https://orcid.org/0009-0007-4503-6073"},"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":"Furkan Eris","raw_affiliation_strings":["Department of Information Technology and Electrical Engineering, ETH Zurich , Zurich, 8092,"],"raw_orcid":"https://orcid.org/0009-0007-4503-6073","affiliations":[{"raw_affiliation_string":"Department of Information Technology and Electrical Engineering, ETH Zurich , Zurich, 8092,","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042072020","display_name":"Jo\u00ebl Lindegger","orcid":"https://orcid.org/0000-0003-2581-8637"},"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":"Joel Lindegger","raw_affiliation_strings":["Department of Information Technology and Electrical Engineering, ETH Zurich , Zurich, 8092,"],"raw_orcid":"https://orcid.org/0000-0003-2581-8637","affiliations":[{"raw_affiliation_string":"Department of Information Technology and Electrical Engineering, ETH Zurich , Zurich, 8092,","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070168682","display_name":"Andr\u00e9 Kahles","orcid":"https://orcid.org/0000-0002-3411-0692"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"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/I4210100468","display_name":"University Hospital of Zurich","ror":"https://ror.org/01462r250","country_code":"CH","type":"funder","lineage":["https://openalex.org/I4210100468"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Andr\u00e9 Kahles","raw_affiliation_strings":["Department of Computer Science, ETH Zurich , Zurich, 8092,","Swiss Institute of Bioinformatics , Zurich, 8057,","University Hospital Zurich , Zurich, 8091,"],"raw_orcid":"https://orcid.org/0000-0002-3411-0692","affiliations":[{"raw_affiliation_string":"Department of Computer Science, ETH Zurich , Zurich, 8092,","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"Swiss Institute of Bioinformatics , Zurich, 8057,","institution_ids":["https://openalex.org/I12708293"]},{"raw_affiliation_string":"University Hospital Zurich , Zurich, 8091,","institution_ids":["https://openalex.org/I4210100468"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5126862742","display_name":"Onur Mutlu","orcid":null},"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":"Onur Mutlu","raw_affiliation_strings":["Department of Information Technology and Electrical Engineering, ETH Zurich , Zurich, 8092,"],"raw_orcid":"https://orcid.org/0000-0002-0075-2312","affiliations":[{"raw_affiliation_string":"Department of Information Technology and Electrical Engineering, ETH Zurich , Zurich, 8092,","institution_ids":["https://openalex.org/I35440088"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":8.7613,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.97144032,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":98},"biblio":{"volume":"42","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11582","display_name":"Nanopore and Nanochannel Transport Studies","score":0.8938000202178955,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11582","display_name":"Nanopore and Nanochannel Transport Studies","score":0.8938000202178955,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10558","display_name":"Advancements in Semiconductor Devices and Circuit Design","score":0.008100000210106373,"subfield":{"id":"https://openalex.org/subfields/2208","display_name":"Electrical and Electronic Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10363","display_name":"Low-power high-performance VLSI design","score":0.005900000222027302,"subfield":{"id":"https://openalex.org/subfields/2208","display_name":"Electrical and Electronic Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/seeding","display_name":"Seeding","score":0.855400025844574},{"id":"https://openalex.org/keywords/nanopore","display_name":"Nanopore","score":0.732699990272522},{"id":"https://openalex.org/keywords/scripting-language","display_name":"Scripting language","score":0.6470000147819519},{"id":"https://openalex.org/keywords/mechanism","display_name":"Mechanism (biology)","score":0.621399998664856},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.3869999945163727}],"concepts":[{"id":"https://openalex.org/C36248471","wikidata":"https://www.wikidata.org/wiki/Q7445669","display_name":"Seeding","level":2,"score":0.855400025844574},{"id":"https://openalex.org/C141795571","wikidata":"https://www.wikidata.org/wiki/Q580942","display_name":"Nanopore","level":2,"score":0.732699990272522},{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.6470000147819519},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6241999864578247},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.621399998664856},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.4823000133037567},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.3869999945163727},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3668000102043152},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.3287000060081482},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.31220000982284546},{"id":"https://openalex.org/C206139338","wikidata":"https://www.wikidata.org/wiki/Q192355","display_name":"Raw material","level":2,"score":0.25679999589920044}],"mesh":[{"descriptor_ui":"D000081414","descriptor_name":"Nanopore Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000081414","descriptor_name":"Nanopore Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058608","descriptor_name":"Nanopores","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058608","descriptor_name":"Nanopores","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058608","descriptor_name":"Nanopores","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058608","descriptor_name":"Nanopores","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btag087","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag087","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41746292","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41746292","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:doi:10.3929/ethz-c-000797361","is_oa":true,"landing_page_url":"http://hdl.handle.net/20.500.11850/797361","pdf_url":null,"source":{"id":"https://openalex.org/S4406922384","display_name":"Open MIND","issn_l":null,"issn":null,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12975284","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12975284/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btag087","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag087","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.4311795234680176,"display_name":"Zero hunger","id":"https://metadata.un.org/sdg/2"}],"awards":[{"id":"https://openalex.org/G2808239538","display_name":null,"funder_award_id":"200021_213084","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G7398905398","display_name":null,"funder_award_id":"#200550","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"}],"funders":[{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":53,"referenced_works":["https://openalex.org/W1519765314","https://openalex.org/W1966822396","https://openalex.org/W1987630123","https://openalex.org/W1997545992","https://openalex.org/W2032145644","https://openalex.org/W2100085677","https://openalex.org/W2100810979","https://openalex.org/W2153325555","https://openalex.org/W2156104322","https://openalex.org/W2194172909","https://openalex.org/W2317495605","https://openalex.org/W2346680365","https://openalex.org/W2463351297","https://openalex.org/W2503273054","https://openalex.org/W2514454343","https://openalex.org/W2607669908","https://openalex.org/W2788228074","https://openalex.org/W2789843538","https://openalex.org/W2792035812","https://openalex.org/W2949279762","https://openalex.org/W2951594770","https://openalex.org/W3002408315","https://openalex.org/W3019659090","https://openalex.org/W3021186977","https://openalex.org/W3047407562","https://openalex.org/W3100933843","https://openalex.org/W3104137212","https://openalex.org/W3109164186","https://openalex.org/W3164465449","https://openalex.org/W3179836387","https://openalex.org/W3183243241","https://openalex.org/W3210810625","https://openalex.org/W3211506914","https://openalex.org/W4283721247","https://openalex.org/W4317625860","https://openalex.org/W4318408334","https://openalex.org/W4319989400","https://openalex.org/W4320503024","https://openalex.org/W4320922321","https://openalex.org/W4376657532","https://openalex.org/W4382918133","https://openalex.org/W4388594766","https://openalex.org/W4389436393","https://openalex.org/W4391883412","https://openalex.org/W4392144321","https://openalex.org/W4400140655","https://openalex.org/W4401107987","https://openalex.org/W4403806354","https://openalex.org/W4405717915","https://openalex.org/W4408934773","https://openalex.org/W7124695987","https://openalex.org/W7125788291","https://openalex.org/W7155696255"],"related_works":[],"abstract_inverted_index":{"MOTIVATION:":[0],"Raw":[1],"nanopore":[2],"signal":[3,54,89],"analysis":[4,16,63],"is":[5,38,58,254],"a":[6,35,42,68,96,148,175,193,239],"common":[7],"approach":[8],"in":[9,51,241],"genomics":[10],"to":[11,21,41,47,59,105,157,170,174,237,263],"provide":[12,260],"fast":[13],"and":[14,155,159,168,189,234],"resource-efficient":[15],"without":[17,24,67,133],"translating":[18],"the":[19,61,77,122,181,261],"signals":[20,32,66,132],"bases":[22,246],"(i.e.":[23],"basecalling).":[25],"However,":[26],"existing":[27,113],"solutions":[28],"cannot":[29],"interpret":[30],"raw":[31,53,65,88,131],"directly":[33,129],"if":[34],"reference":[36,69],"genome":[37,177],"unknown":[39],"due":[40],"lack":[43],"of":[44,64,84,141,200],"accurate":[45,227],"mechanisms":[46],"handle":[48],"increased":[49],"noise":[50],"pairwise":[52],"comparison.":[55],"Our":[56,135],"goal":[57],"enable":[60],"direct":[62],"genome.":[70],"To":[71,117],"this":[72],"end,":[73],"we":[74,213,219],"propose":[75],"Rawsamble,":[76,218],"first":[78,123],"mechanism":[79],"that":[80,145,197,211,223],"can":[81,220],"identify":[82],"regions":[83],"similarity":[85],"between":[86],"all":[87],"pairs,":[90],"known":[91],"as":[92,226,228],"all-vs-all":[93],"overlapping,":[94],"using":[95,180],"hash-based":[97],"search":[98],"mechanism.":[99],"RESULTS:":[100],"We":[101,195,209,258],"use":[102,214],"these":[103,120],"overlaps":[104,233],"construct":[106,221],"de":[107,124],"novo":[108,125],"assembly":[109,178],"graphs":[110],"with":[111],"an":[112],"assembler,":[114],"miniasm,":[115],"off-the-shelf.":[116],"our":[118,266,269],"knowledge,":[119],"are":[121,204,224],"assemblies":[126],"ever":[127],"constructed":[128],"from":[130,217,231],"basecalling.":[134],"extensive":[136],"evaluations":[137],"across":[138],"multiple":[139],"genomes":[140],"varying":[142],"sizes":[143],"show":[144],"Rawsamble":[146,253],"provides":[147],"significant":[149],"speedup":[150],"(on":[151,164],"average":[152,165],"by":[153,166,171,207],"5.01\u00d7":[154],"up":[156,169,236],"23.10\u00d7)":[158],"reduces":[160],"peak":[161],"memory":[162],"usage":[163],"5.74\u00d7":[167],"22.00\u00d7)":[172],"compared":[173],"conventional":[176],"pipeline":[179],"state-of-the-art":[182],"tools":[183],"for":[184,247],"basecalling":[185],"(Dorado's":[186],"fastest":[187],"mode)":[188],"overlapping":[190,202,215],"(minimap2)":[191],"on":[192,268],"CPU.":[194],"find":[196,210],"around":[198],"one-third":[199],"Rawsamble's":[201],"pairs":[203],"also":[205,259],"found":[206],"minimap2.":[208],"when":[212],"reads":[216],"unitigs":[222],"(i)":[225],"those":[229],"built":[230],"minimap2's":[232],"(ii)":[235],"half":[238],"chromosome":[240],"length":[242],"(e.g.":[243],"2.3":[244],"million":[245],"E.":[248],"coli).":[249],"AVAILABILITY":[250],"AND":[251],"IMPLEMENTATION:":[252],"available":[255],"at":[256],"https://github.com/CMU-SAFARI/RawHash.":[257],"scripts":[262],"fully":[264],"reproduce":[265],"results":[267],"GitHub":[270],"page.":[271]},"counts_by_year":[{"year":2026,"cited_by_count":2}],"updated_date":"2026-07-12T07:33:03.550515","created_date":"2026-02-27T00:00:00"}
