{"id":"https://openalex.org/W2949074065","doi":"https://doi.org/10.1093/bioinformatics/btz461","title":"Nanopype: a modular and scalable nanopore data processing pipeline","display_name":"Nanopype: a modular and scalable nanopore data processing pipeline","publication_year":2019,"publication_date":"2019-06-07","ids":{"openalex":"https://openalex.org/W2949074065","doi":"https://doi.org/10.1093/bioinformatics/btz461","mag":"2949074065","pmid":"https://pubmed.ncbi.nlm.nih.gov/31192347"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz461","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz461","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/22/4770/30706903/btz461.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":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/35/22/4770/30706903/btz461.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5034653999","display_name":"Pay Gie\u00dfelmann","orcid":"https://orcid.org/0000-0002-1227-897X"},"institutions":[{"id":"https://openalex.org/I4210142260","display_name":"Max Planck Institute for Molecular Genetics","ror":"https://ror.org/03ate3e03","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210142260"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Pay Giesselmann","raw_affiliation_strings":["Department of Genome Regulation, Max Planck Institute for Molecular Genetics , Berlin, Germany"],"affiliations":[{"raw_affiliation_string":"Department of Genome Regulation, Max Planck Institute for Molecular Genetics , Berlin, Germany","institution_ids":["https://openalex.org/I4210142260"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089751173","display_name":"Sara Hetzel","orcid":"https://orcid.org/0000-0002-4783-3814"},"institutions":[{"id":"https://openalex.org/I4210142260","display_name":"Max Planck Institute for Molecular Genetics","ror":"https://ror.org/03ate3e03","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210142260"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Sara Hetzel","raw_affiliation_strings":["Department of Genome Regulation, Max Planck Institute for Molecular Genetics , Berlin, Germany"],"affiliations":[{"raw_affiliation_string":"Department of Genome Regulation, Max Planck Institute for Molecular Genetics , Berlin, Germany","institution_ids":["https://openalex.org/I4210142260"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112766589","display_name":"Frank M\u00fcller","orcid":"https://orcid.org/0000-0001-9478-8430"},"institutions":[{"id":"https://openalex.org/I9341345","display_name":"University of L\u00fcbeck","ror":"https://ror.org/00t3r8h32","country_code":"DE","type":"education","lineage":["https://openalex.org/I9341345"]},{"id":"https://openalex.org/I4210112713","display_name":"University Hospital Schleswig-Holstein","ror":"https://ror.org/01tvm6f46","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210112713"]},{"id":"https://openalex.org/I4210142260","display_name":"Max Planck Institute for Molecular Genetics","ror":"https://ror.org/03ate3e03","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210142260"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Franz-Josef M\u00fcller","raw_affiliation_strings":["Department of Genome Regulation, Max Planck Institute for Molecular Genetics , Berlin, Germany","Department of Psychiatry and Psychotherapy, Zentrum f\u00fcr Integrative Psychiatrie gGmbH, Universit\u00e4tsklinikum Schleswig-Holstein , Campus Kiel, Kiel, Germany"],"affiliations":[{"raw_affiliation_string":"Department of Genome Regulation, Max Planck Institute for Molecular Genetics , Berlin, Germany","institution_ids":["https://openalex.org/I4210142260"]},{"raw_affiliation_string":"Department of Psychiatry and Psychotherapy, Zentrum f\u00fcr Integrative Psychiatrie gGmbH, Universit\u00e4tsklinikum Schleswig-Holstein , Campus Kiel, Kiel, Germany","institution_ids":["https://openalex.org/I4210112713","https://openalex.org/I9341345"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031703305","display_name":"Alexander Meissner","orcid":"https://orcid.org/0000-0001-8646-7469"},"institutions":[{"id":"https://openalex.org/I4210142260","display_name":"Max Planck Institute for Molecular Genetics","ror":"https://ror.org/03ate3e03","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210142260"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Alexander Meissner","raw_affiliation_strings":["Department of Genome Regulation, Max Planck Institute for Molecular Genetics , Berlin, Germany"],"affiliations":[{"raw_affiliation_string":"Department of Genome Regulation, Max Planck Institute for Molecular Genetics , Berlin, Germany","institution_ids":["https://openalex.org/I4210142260"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5089743337","display_name":"Helene Kretzmer","orcid":"https://orcid.org/0000-0002-0723-4980"},"institutions":[{"id":"https://openalex.org/I4210142260","display_name":"Max Planck Institute for Molecular Genetics","ror":"https://ror.org/03ate3e03","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210142260"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Helene Kretzmer","raw_affiliation_strings":["Department of Genome Regulation, Max Planck Institute for Molecular Genetics , Berlin, Germany"],"affiliations":[{"raw_affiliation_string":"Department of Genome Regulation, Max Planck Institute for Molecular Genetics , Berlin, Germany","institution_ids":["https://openalex.org/I4210142260"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5031703305"],"corresponding_institution_ids":["https://openalex.org/I4210142260"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.6871,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":{"value":0.68910982,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"35","issue":"22","first_page":"4770","last_page":"4772"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9965000152587891,"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":0.9965000152587891,"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":0.9736999869346619,"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/T11269","display_name":"Algorithms and Data Compression","score":0.9495000243186951,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8290446996688843},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.7810345888137817},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.7719336748123169},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.607483983039856},{"id":"https://openalex.org/keywords/modular-design","display_name":"Modular design","score":0.5836801528930664},{"id":"https://openalex.org/keywords/nanopore-sequencing","display_name":"Nanopore sequencing","score":0.5641805529594421},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.511242151260376},{"id":"https://openalex.org/keywords/throughput","display_name":"Throughput","score":0.5002033710479736},{"id":"https://openalex.org/keywords/nanopore","display_name":"Nanopore","score":0.4674447774887085},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.35259202122688293},{"id":"https://openalex.org/keywords/computer-architecture","display_name":"Computer architecture","score":0.34299737215042114},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.23631033301353455},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.20198607444763184},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.15135392546653748},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.11071917414665222},{"id":"https://openalex.org/keywords/nanotechnology","display_name":"Nanotechnology","score":0.09837198257446289}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8290446996688843},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7810345888137817},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7719336748123169},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.607483983039856},{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.5836801528930664},{"id":"https://openalex.org/C126513998","wikidata":"https://www.wikidata.org/wiki/Q8973627","display_name":"Nanopore sequencing","level":4,"score":0.5641805529594421},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.511242151260376},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.5002033710479736},{"id":"https://openalex.org/C141795571","wikidata":"https://www.wikidata.org/wiki/Q580942","display_name":"Nanopore","level":2,"score":0.4674447774887085},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.35259202122688293},{"id":"https://openalex.org/C118524514","wikidata":"https://www.wikidata.org/wiki/Q173212","display_name":"Computer architecture","level":1,"score":0.34299737215042114},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.23631033301353455},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.20198607444763184},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.15135392546653748},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.11071917414665222},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.09837198257446289},{"id":"https://openalex.org/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"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/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","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/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.0}],"mesh":[{"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":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btz461","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz461","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/22/4770/30706903/btz461.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:31192347","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31192347","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":"pmid:31386105","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31386105","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:pure.mpg.de:item_3164012","is_oa":true,"landing_page_url":"http://hdl.handle.net/21.11116/0000-0004-A985-7","pdf_url":null,"source":{"id":"https://openalex.org/S4306400654","display_name":"MPG.PuRe (Max Planck Society)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I149899117","host_organization_name":"Max Planck Society","host_organization_lineage":["https://openalex.org/I149899117"],"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":"Bioinformatics","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btz461","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz461","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/22/4770/30706903/btz461.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/F4320308022","display_name":"California Department of Fish and Game","ror":"https://ror.org/02v6w2r95"},{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320322434","display_name":"Max-Planck-Gesellschaft","ror":"https://ror.org/01hhn8329"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2949074065.pdf","grobid_xml":"https://content.openalex.org/works/W2949074065.grobid-xml"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W757829720","https://openalex.org/W2102619694","https://openalex.org/W2108234281","https://openalex.org/W2110417468","https://openalex.org/W2129785061","https://openalex.org/W2337261418","https://openalex.org/W2591367881","https://openalex.org/W2625641149","https://openalex.org/W2789843538","https://openalex.org/W2881827384","https://openalex.org/W2950121474","https://openalex.org/W6739789898","https://openalex.org/W6748810007"],"related_works":["https://openalex.org/W2774675543","https://openalex.org/W2119052929","https://openalex.org/W2326282944","https://openalex.org/W2330402197","https://openalex.org/W3197006535","https://openalex.org/W3201371206","https://openalex.org/W2420153309","https://openalex.org/W3175842380","https://openalex.org/W2107323267","https://openalex.org/W2589591413"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
