{"id":"https://openalex.org/W4405222779","doi":"https://doi.org/10.1093/bioinformatics/btae665","title":"Pod5Viewer: a GUI for inspecting raw nanopore sequencing data","display_name":"Pod5Viewer: a GUI for inspecting raw nanopore sequencing data","publication_year":2024,"publication_date":"2024-11-28","ids":{"openalex":"https://openalex.org/W4405222779","doi":"https://doi.org/10.1093/bioinformatics/btae665","pmid":"https://pubmed.ncbi.nlm.nih.gov/39657315"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae665","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae665","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/btae665","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5007330724","display_name":"Vincent Dietrich","orcid":"https://orcid.org/0000-0003-0568-9727"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]},{"id":"https://openalex.org/I4210094062","display_name":"University Medical Center of the Johannes Gutenberg University Mainz","ror":"https://ror.org/00q1fsf04","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210094062"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Vincent Dietrich","raw_affiliation_strings":["Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz , Mainz, 55128,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz , Mainz, 55128,","institution_ids":["https://openalex.org/I4210094062","https://openalex.org/I197323543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070814314","display_name":"Nicol\u00f2 Alagna","orcid":null},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]},{"id":"https://openalex.org/I4210094062","display_name":"University Medical Center of the Johannes Gutenberg University Mainz","ror":"https://ror.org/00q1fsf04","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210094062"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Nicol\u00f2 Alagna","raw_affiliation_strings":["Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz , Mainz, 55128,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz , Mainz, 55128,","institution_ids":["https://openalex.org/I4210094062","https://openalex.org/I197323543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001477363","display_name":"Mark Helm","orcid":"https://orcid.org/0000-0002-0154-0928"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Mark Helm","raw_affiliation_strings":["Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz , Mainz, 55128,"],"raw_orcid":"https://orcid.org/0000-0002-0154-0928","affiliations":[{"raw_affiliation_string":"Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz , Mainz, 55128,","institution_ids":["https://openalex.org/I197323543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006364288","display_name":"Susanne Gerber","orcid":"https://orcid.org/0000-0001-9513-0729"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]},{"id":"https://openalex.org/I4210094062","display_name":"University Medical Center of the Johannes Gutenberg University Mainz","ror":"https://ror.org/00q1fsf04","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210094062"]},{"id":"https://openalex.org/I4210098931","display_name":"Quantitative BioSciences","ror":"https://ror.org/010brsj79","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210098931"]}],"countries":["DE","US"],"is_corresponding":false,"raw_author_name":"Susanne Gerber","raw_affiliation_strings":["Institute for Quantitative and Computational Biosciences (IQCB) , Johannes-von-M\u00fcller-Weg 6, Mainz, 55128,","Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz , Mainz, 55128,"],"raw_orcid":"https://orcid.org/0000-0001-9513-0729","affiliations":[{"raw_affiliation_string":"Institute for Quantitative and Computational Biosciences (IQCB) , Johannes-von-M\u00fcller-Weg 6, Mainz, 55128,","institution_ids":["https://openalex.org/I4210098931"]},{"raw_affiliation_string":"Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz , Mainz, 55128,","institution_ids":["https://openalex.org/I4210094062","https://openalex.org/I197323543"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064602514","display_name":"Tamer Butto","orcid":"https://orcid.org/0000-0001-8028-0038"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Tamer Butto","raw_affiliation_strings":["Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz , Mainz, 55128,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz , Mainz, 55128,","institution_ids":["https://openalex.org/I197323543"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"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":0.3203,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.5594041,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":98},"biblio":{"volume":"40","issue":"12","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":0.3853999972343445,"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":0.3853999972343445,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.20160000026226044,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.06539999693632126,"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":0.7179588675498962},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6775414943695068},{"id":"https://openalex.org/keywords/nanopore","display_name":"Nanopore","score":0.6576887369155884},{"id":"https://openalex.org/keywords/raw-data","display_name":"Raw data","score":0.560685396194458},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.44417837262153625},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2121969759464264},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.179539293050766},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1402769684791565},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.13390865921974182},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09578177332878113},{"id":"https://openalex.org/keywords/chemical-engineering","display_name":"Chemical engineering","score":0.0656728446483612},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.06232792139053345}],"concepts":[{"id":"https://openalex.org/C126513998","wikidata":"https://www.wikidata.org/wiki/Q8973627","display_name":"Nanopore sequencing","level":4,"score":0.7179588675498962},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6775414943695068},{"id":"https://openalex.org/C141795571","wikidata":"https://www.wikidata.org/wiki/Q580942","display_name":"Nanopore","level":2,"score":0.6576887369155884},{"id":"https://openalex.org/C132964779","wikidata":"https://www.wikidata.org/wiki/Q2110223","display_name":"Raw data","level":2,"score":0.560685396194458},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.44417837262153625},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2121969759464264},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.179539293050766},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1402769684791565},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.13390865921974182},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09578177332878113},{"id":"https://openalex.org/C42360764","wikidata":"https://www.wikidata.org/wiki/Q83588","display_name":"Chemical engineering","level":1,"score":0.0656728446483612},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.06232792139053345}],"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":"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":"D000081414","descriptor_name":"Nanopore Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","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":"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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058608","descriptor_name":"Nanopores","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":false},{"descriptor_ui":"D058608","descriptor_name":"Nanopores","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":false},{"descriptor_ui":"D058608","descriptor_name":"Nanopores","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae665","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae665","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:39657315","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39657315","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:pubmedcentral.nih.gov:11630908","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11630908","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11630908/pdf/btae665.pdf","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/btae665","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae665","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":[],"awards":[{"id":"https://openalex.org/G1574603548","display_name":null,"funder_award_id":"SFB 1552","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G297554700","display_name":null,"funder_award_id":"439669440-TRR 319","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G5035700077","display_name":"TRR 319: RMaP: RNA Modifikation und Prozessierung","funder_award_id":"439669440","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G6475466669","display_name":null,"funder_award_id":"TRR 319","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G7151617741","display_name":"SFB 1552: Defekte und Defektkontrolle in weicher Materie","funder_award_id":"465145163","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":4,"referenced_works":["https://openalex.org/W3213101281","https://openalex.org/W4205752547","https://openalex.org/W4385680865","https://openalex.org/W4400981569"],"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":{"MOTIVATION:":[0],"Oxford":[1],"Nanopore":[2],"Technologies":[3],"recently":[4],"adopted":[5],"the":[6,26,31,38,42,59,99,127],"POD5":[7,66,82],"file":[8],"format":[9],"for":[10,48,64,87,110],"storing":[11],"raw":[12,34,75],"nanopore":[13,35],"sequencing":[14,27,76],"data.":[15,36],"The":[16,69,119],"information":[17],"stored":[18],"in":[19,81,97],"these":[20],"files":[21],"provides":[22],"detailed":[23],"insights":[24],"into":[25],"features":[28],"and":[29,78,90,105],"enhances":[30],"understanding":[32],"of":[33,40],"However,":[37],"process":[39],"visualizing":[41],"data":[43,77],"can":[44],"be":[45],"cumbersome,":[46],"especially":[47],"users":[49,111],"without":[50],"programming":[51],"skills.":[52],"To":[53],"address":[54],"this":[55],"issue,":[56],"we":[57],"developed":[58],"pod5Viewer,":[60],"a":[61],"GUI":[62],"application":[63],"inspecting":[65],"files.":[67,83],"RESULTS:":[68],"pod5Viewer":[70,100,120,128],"offers":[71],"straightforward":[72],"access":[73],"to":[74,103],"associated":[79],"metadata":[80],"It":[84],"includes":[85],"functionalities":[86],"viewing,":[88],"plotting,":[89],"exporting":[91],"individual":[92],"reads.":[93],"Designed":[94],"with":[95,112],"user-friendliness":[96],"mind,":[98],"is":[101,121],"easy":[102],"install":[104],"use,":[106],"making":[107],"it":[108],"suitable":[109],"all":[113],"technical":[114],"backgrounds.":[115],"AVAILABILITY":[116],"AND":[117],"IMPLEMENTATION:":[118],"available":[122],"as":[123],"open":[124],"source":[125],"from":[126],"Github":[129],"repository":[130],"(https://github.com/dietvin/pod5Viewer).":[131]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1}],"updated_date":"2026-06-22T08:00:12.763002","created_date":"2025-10-10T00:00:00"}