{"id":"https://openalex.org/W2792035812","doi":"https://doi.org/10.1093/bib/bby017","title":"Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions","display_name":"Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions","publication_year":2018,"publication_date":"2018-02-25","ids":{"openalex":"https://openalex.org/W2792035812","doi":"https://doi.org/10.1093/bib/bby017","mag":"2792035812","pmid":"https://pubmed.ncbi.nlm.nih.gov/29617724"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bby017","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bby017","pdf_url":"https://academic.oup.com/bib/advance-article-pdf/doi/10.1093/bib/bby017/24523838/bby017.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"review","indexed_in":["arxiv","crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/advance-article-pdf/doi/10.1093/bib/bby017/24523838/bby017.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Damla Senol Cali","orcid":"https://orcid.org/0000-0002-0075-2312"},"institutions":[{"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":["US"],"is_corresponding":true,"raw_author_name":"Damla Senol Cali","raw_affiliation_strings":["Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA, USA"],"raw_orcid":"https://orcid.org/0000-0002-0075-2312","affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040743445","display_name":"Jeremie S. Kim","orcid":"https://orcid.org/0000-0001-6153-9008"},"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/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["CH","US"],"is_corresponding":false,"raw_author_name":"Jeremie S Kim","raw_affiliation_strings":["Department of Computer Science, Systems Group, ETH Z\u00fcrich, Z\u00fcrich, Switzerland","Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Systems Group, ETH Z\u00fcrich, Z\u00fcrich, Switzerland","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036666743","display_name":"Saugata Ghose","orcid":"https://orcid.org/0000-0002-9138-0613"},"institutions":[{"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":["US"],"is_corresponding":false,"raw_author_name":"Saugata Ghose","raw_affiliation_strings":["Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I74973139"]}]},{"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":false,"raw_author_name":"Can Alkan","raw_affiliation_strings":["Department of Computer Engineering, Bilkent University, Bilkent, Ankara, Turkey"],"raw_orcid":"https://orcid.org/0000-0002-5443-0706","affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Bilkent University, Bilkent, 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/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","US"],"is_corresponding":false,"raw_author_name":"Onur Mutlu","raw_affiliation_strings":["Department of Computer Science, Systems Group, ETH Z\u00fcrich, Z\u00fcrich, Switzerland","Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Systems Group, ETH Z\u00fcrich, Z\u00fcrich, Switzerland","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I74973139"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I74973139"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":13.218,"has_fulltext":true,"cited_by_count":258,"citation_normalized_percentile":{"value":0.99323356,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"20","issue":"4","first_page":"1542","last_page":"1559"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991000294685364,"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":0.9991000294685364,"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/T11582","display_name":"Nanopore and Nanochannel Transport Studies","score":0.9887999892234802,"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/T11482","display_name":"RNA modifications and cancer","score":0.9822999835014343,"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/nanopore-sequencing","display_name":"Nanopore sequencing","score":0.8500365018844604},{"id":"https://openalex.org/keywords/software-portability","display_name":"Software portability","score":0.7793844938278198},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7697776556015015},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.6994091868400574},{"id":"https://openalex.org/keywords/nanopore","display_name":"Nanopore","score":0.689089298248291},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.6205503940582275},{"id":"https://openalex.org/keywords/sequence-assembly","display_name":"Sequence assembly","score":0.5112509727478027},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4254026412963867},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4195255637168884},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.39464741945266724},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.36715972423553467},{"id":"https://openalex.org/keywords/nanotechnology","display_name":"Nanotechnology","score":0.16973033547401428},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09937378764152527},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.07130759954452515}],"concepts":[{"id":"https://openalex.org/C126513998","wikidata":"https://www.wikidata.org/wiki/Q8973627","display_name":"Nanopore sequencing","level":4,"score":0.8500365018844604},{"id":"https://openalex.org/C63000827","wikidata":"https://www.wikidata.org/wiki/Q3080428","display_name":"Software portability","level":2,"score":0.7793844938278198},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7697776556015015},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6994091868400574},{"id":"https://openalex.org/C141795571","wikidata":"https://www.wikidata.org/wiki/Q580942","display_name":"Nanopore","level":2,"score":0.689089298248291},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.6205503940582275},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.5112509727478027},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4254026412963867},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4195255637168884},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.39464741945266724},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.36715972423553467},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.16973033547401428},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09937378764152527},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.07130759954452515},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.0},{"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/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"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/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000081414","descriptor_name":"Nanopore Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000081414","descriptor_name":"Nanopore Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000081414","descriptor_name":"Nanopore Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000081414","descriptor_name":"Nanopore Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000081414","descriptor_name":"Nanopore Sequencing","qualifier_ui":"Q000639","qualifier_name":"trends","is_major_topic":false},{"descriptor_ui":"D000081414","descriptor_name":"Nanopore Sequencing","qualifier_ui":"Q000639","qualifier_name":"trends","is_major_topic":false},{"descriptor_ui":"D000081414","descriptor_name":"Nanopore Sequencing","qualifier_ui":"Q000639","qualifier_name":"trends","is_major_topic":false},{"descriptor_ui":"D000081414","descriptor_name":"Nanopore Sequencing","qualifier_ui":"Q000639","qualifier_name":"trends","is_major_topic":false},{"descriptor_ui":"D000081414","descriptor_name":"Nanopore Sequencing","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D000081414","descriptor_name":"Nanopore Sequencing","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D000081414","descriptor_name":"Nanopore Sequencing","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D000081414","descriptor_name":"Nanopore Sequencing","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000639","qualifier_name":"trends","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000639","qualifier_name":"trends","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000639","qualifier_name":"trends","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000639","qualifier_name":"trends","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1093/bib/bby017","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bby017","pdf_url":"https://academic.oup.com/bib/advance-article-pdf/doi/10.1093/bib/bby017/24523838/bby017.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:29617724","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29617724","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:arXiv.org:1711.08774","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1711.08774","pdf_url":"https://arxiv.org/pdf/1711.08774","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":"pmh:oai:pubmedcentral.nih.gov:6781587","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6781587","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"},{"id":"pmh:oai:repository.bilkent.edu.tr:11693/50560","is_oa":false,"landing_page_url":"http://hdl.handle.net/11693/50560","pdf_url":null,"source":{"id":"https://openalex.org/S4306400079","display_name":"Bilkent University Institutional Repository (Bilkent University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I168864056","host_organization_name":"Bilkent University","host_organization_lineage":["https://openalex.org/I168864056"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Briefings in Bioinformatics","raw_type":"Review"},{"id":"pmh:oai:www.research-collection.ethz.ch:20.500.11850/313591","is_oa":true,"landing_page_url":"http://hdl.handle.net/20.500.11850/313591","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Briefings in Bioinformatics, 20 (4)","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"doi:10.3929/ethz-b-000313591","is_oa":true,"landing_page_url":"https://doi.org/10.3929/ethz-b-000313591","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/bib/bby017","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bby017","pdf_url":"https://academic.oup.com/bib/advance-article-pdf/doi/10.1093/bib/bby017/24523838/bby017.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.5,"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9"}],"awards":[{"id":"https://openalex.org/G2814824731","display_name":null,"funder_award_id":"EMBO-IG 2521","funder_id":"https://openalex.org/F4320307844","funder_display_name":"European Molecular Biology Organization"},{"id":"https://openalex.org/G4539561046","display_name":null,"funder_award_id":"HG006004","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320307102","display_name":"Intel Corporation","ror":"https://ror.org/01ek73717"},{"id":"https://openalex.org/F4320307844","display_name":"European Molecular Biology Organization","ror":"https://ror.org/04wfr2810"},{"id":"https://openalex.org/F4320309327","display_name":"Google","ror":"https://ror.org/00njsd438"},{"id":"https://openalex.org/F4320316785","display_name":"VMware","ror":null},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332195","display_name":"Samsung","ror":"https://ror.org/04w3jy968"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2792035812.pdf","grobid_xml":"https://content.openalex.org/works/W2792035812.grobid-xml"},"referenced_works_count":95,"referenced_works":["https://openalex.org/W87616783","https://openalex.org/W1519765314","https://openalex.org/W1552648004","https://openalex.org/W1828154403","https://openalex.org/W1873119440","https://openalex.org/W1917192789","https://openalex.org/W1953000621","https://openalex.org/W1997246534","https://openalex.org/W2000586119","https://openalex.org/W2015292449","https://openalex.org/W2021724381","https://openalex.org/W2025583382","https://openalex.org/W2026861756","https://openalex.org/W2041391522","https://openalex.org/W2046137036","https://openalex.org/W2061338306","https://openalex.org/W2082825869","https://openalex.org/W2084821192","https://openalex.org/W2091193685","https://openalex.org/W2095680943","https://openalex.org/W2103441770","https://openalex.org/W2108058966","https://openalex.org/W2108234281","https://openalex.org/W2112113834","https://openalex.org/W2114133992","https://openalex.org/W2116020886","https://openalex.org/W2117608012","https://openalex.org/W2120230074","https://openalex.org/W2121364424","https://openalex.org/W2121716038","https://openalex.org/W2121762798","https://openalex.org/W2124985265","https://openalex.org/W2127407003","https://openalex.org/W2129714591","https://openalex.org/W2130942839","https://openalex.org/W2131774270","https://openalex.org/W2136651963","https://openalex.org/W2138708064","https://openalex.org/W2139747296","https://openalex.org/W2140154634","https://openalex.org/W2142113273","https://openalex.org/W2142384583","https://openalex.org/W2143503258","https://openalex.org/W2144037940","https://openalex.org/W2146496959","https://openalex.org/W2153527981","https://openalex.org/W2162055898","https://openalex.org/W2165293958","https://openalex.org/W2168303240","https://openalex.org/W2169040626","https://openalex.org/W2194172909","https://openalex.org/W2259815689","https://openalex.org/W2269938998","https://openalex.org/W2317495605","https://openalex.org/W2337261418","https://openalex.org/W2514454343","https://openalex.org/W2516652149","https://openalex.org/W2521004200","https://openalex.org/W2560228154","https://openalex.org/W2566610827","https://openalex.org/W2575750030","https://openalex.org/W2581118389","https://openalex.org/W2591367881","https://openalex.org/W2607669908","https://openalex.org/W2625641149","https://openalex.org/W2731064643","https://openalex.org/W2745167386","https://openalex.org/W2749642998","https://openalex.org/W2755804176","https://openalex.org/W2762638728","https://openalex.org/W2766890412","https://openalex.org/W2772019197","https://openalex.org/W2949097965","https://openalex.org/W2949279762","https://openalex.org/W2950354111","https://openalex.org/W2950548676","https://openalex.org/W2950993016","https://openalex.org/W2952788979","https://openalex.org/W2953329757","https://openalex.org/W3103269557","https://openalex.org/W3142147837","https://openalex.org/W3147254695","https://openalex.org/W3207400511","https://openalex.org/W4237941914","https://openalex.org/W4245955616","https://openalex.org/W4247053599","https://openalex.org/W4394655901","https://openalex.org/W4394666350","https://openalex.org/W6603439255","https://openalex.org/W6628896446","https://openalex.org/W6681342780","https://openalex.org/W6732206172","https://openalex.org/W6740813679","https://openalex.org/W6742297727","https://openalex.org/W6743444797"],"related_works":["https://openalex.org/W2774675543","https://openalex.org/W2119052929","https://openalex.org/W2326282944","https://openalex.org/W2330402197","https://openalex.org/W2420153309","https://openalex.org/W3201371206","https://openalex.org/W3175842380","https://openalex.org/W2096970964","https://openalex.org/W2107323267","https://openalex.org/W2589591413"],"abstract_inverted_index":{"Nanopore":[0],"sequencing":[1,9,164,346],"technology":[2,28],"has":[3,182],"the":[4,27,52,57,90,107,111,115,129,145,148,158,205,209,238,275,304,314,324,339,344],"potential":[5],"to":[6,15,65,76,87,97,236,242,337],"render":[7],"other":[8],"technologies":[10],"obsolete":[11],"with":[12,313],"its":[13],"ability":[14],"generate":[16],"long":[17],"reads":[18],"and":[19,81,110,123,172,187,200,226,273,282,292,297,335],"provide":[20,125],"portability.":[21],"However,":[22,180],"high":[23,53,159,340],"error":[24,54,160,341],"rates":[25,55,161,342],"of":[26,45,56,147,162,178,234,270,303,316,343],"pose":[29],"a":[30,153,183,196,258],"challenge":[31],"while":[32,256],"generating":[33],"accurate":[34,216,334],"genome":[35,116,305],"assemblies.":[36],"The":[37,212,247],"tools":[38,71,92,113,131,272,326],"used":[39,221],"for":[40,72,127,132,150,208,222,300],"nanopore":[41,73,120,163,309,345],"sequence":[42,74,121,310],"analysis":[43,75],"are":[44,332],"critical":[46,154],"importance,":[47],"as":[48],"they":[49],"should":[50],"overcome":[51,338],"technology.":[58,165,347],"Our":[59],"goal":[60],"in":[61,114,156,176,294],"this":[62,102],"work":[63],"is":[64,85,189,195],"comprehensively":[66],"analyze":[67,106,267],"current":[68,91,325],"publicly":[69],"available":[70],"understand":[77,88],"their":[78],"advantages,":[79],"disadvantages":[80],"performance":[82,201],"bottlenecks.":[83],"It":[84],"important":[86],"where":[89],"do":[93],"not":[94],"perform":[95,174],"well":[96],"develop":[98],"better":[99],"tools.":[100],"To":[101],"end,":[103],"we":[104,139,318],"(1)":[105,144],"multiple":[108],"steps":[109],"associated":[112],"assembly":[117,210,306],"pipeline":[118,307],"using":[119,308],"data,":[122],"(2)":[124,166],"guidelines":[126],"determining":[128],"appropriate":[130,206],"each":[133,301],"step.":[134,211],"Based":[135],"on":[136,204,232],"our":[137,287],"analyses,":[138],"make":[140],"four":[141],"key":[142],"observations:":[143],"choice":[146],"tool":[149,207],"basecalling":[151],"plays":[152],"role":[155],"overcoming":[157],"Read-to-read":[167],"overlap":[168],"finding":[169],"tools,":[170],"GraphMap":[171],"Minimap,":[173],"similarly":[175],"terms":[177],"accuracy.":[179],"Minimap":[181],"lower":[184],"memory":[185,280],"usage,":[186],"it":[188,235],"faster":[190,243],"than":[191],"GraphMap.":[192],"(3)":[193],"There":[194],"trade-off":[197],"between":[198,277],"accuracy":[199],"when":[202],"deciding":[203],"fast":[213],"but":[214],"less":[215],"assembler":[217],"Miniasm":[218],"can":[219,229,289,322],"be":[220,230],"quick":[223],"initial":[224],"assembly,":[225],"further":[227],"polishing":[228,249,263],"applied":[231],"top":[233],"increase":[237],"accuracy,":[239,278],"which":[240],"leads":[241],"overall":[244],"assembly.":[245],"(4)":[246],"state-of-the-art":[248],"tool,":[250,264],"Racon,":[251],"generates":[252],"high-quality":[253],"consensus":[254],"sequences":[255],"providing":[257],"significant":[259],"speedup":[260],"over":[261],"another":[262],"Nanopolish.":[265],"We":[266,284],"various":[268],"combinations":[269],"different":[271],"expose":[274],"trade-offs":[276],"performance,":[279],"usage":[281],"scalability.":[283],"conclude":[285],"that":[286,331],"observations":[288],"guide":[290],"researchers":[291],"practitioners":[293],"making":[295],"conscious":[296],"effective":[298],"choices":[299],"step":[302],"data.":[311],"Also,":[312],"help":[315],"bottlenecks":[317],"have":[319],"found,":[320],"developers":[321],"improve":[323],"or":[327],"build":[328],"new":[329],"ones":[330],"both":[333],"fast,":[336]},"counts_by_year":[{"year":2026,"cited_by_count":8},{"year":2025,"cited_by_count":16},{"year":2024,"cited_by_count":35},{"year":2023,"cited_by_count":27},{"year":2022,"cited_by_count":35},{"year":2021,"cited_by_count":66},{"year":2020,"cited_by_count":36},{"year":2019,"cited_by_count":24},{"year":2018,"cited_by_count":10}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2018-03-29T00:00:00"}