{"id":"https://openalex.org/W7172328242","doi":"https://doi.org/10.1093/bioinformatics/btag518","title":"NextLongIso: a comprehensive Nextflow pipeline for multi-dimensional long-read RNA-seq analysis","display_name":"NextLongIso: a comprehensive Nextflow pipeline for multi-dimensional long-read RNA-seq analysis","publication_year":2026,"publication_date":"2026-08-01","ids":{"openalex":"https://openalex.org/W7172328242","doi":"https://doi.org/10.1093/bioinformatics/btag518","pmid":"https://pubmed.ncbi.nlm.nih.gov/42544764"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btag518","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag518","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/btag518","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5144248964","display_name":"Jiang Tan","orcid":null},"institutions":[{"id":"https://openalex.org/I114277686","display_name":"James S. McDonnell Foundation","ror":"https://ror.org/03dy4aq19","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I114277686"]},{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]},{"id":"https://openalex.org/I4210163477","display_name":"Institute for Medical Informatics and Biostatistics","ror":"https://ror.org/04e79zk25","country_code":"CH","type":"facility","lineage":["https://openalex.org/I4210163477"]}],"countries":["CH","US"],"is_corresponding":false,"raw_author_name":"Jiang Tan","raw_affiliation_strings":["Center for Translational Bioinformatics, Washington University School of Medicine , St. Louis, MO,","Department of Genetics, Washington University School of Medicine , St. Louis, MO,","Institute for Informatics, Data Science and Biostatistics, Washington University School of Medicine , Saint Louis, MO,","McDonnell Genome Institute, Washington University School of Medicine , St. Louis, MO,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Translational Bioinformatics, Washington University School of Medicine , St. Louis, MO,","institution_ids":["https://openalex.org/I204465549"]},{"raw_affiliation_string":"Department of Genetics, Washington University School of Medicine , St. Louis, MO,","institution_ids":["https://openalex.org/I204465549"]},{"raw_affiliation_string":"Institute for Informatics, Data Science and Biostatistics, Washington University School of Medicine , Saint Louis, MO,","institution_ids":["https://openalex.org/I4210163477"]},{"raw_affiliation_string":"McDonnell Genome Institute, Washington University School of Medicine , St. Louis, MO,","institution_ids":["https://openalex.org/I114277686"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064300490","display_name":"Yuqing Wu","orcid":null},"institutions":[{"id":"https://openalex.org/I114277686","display_name":"James S. McDonnell Foundation","ror":"https://ror.org/03dy4aq19","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I114277686"]},{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]},{"id":"https://openalex.org/I4210163477","display_name":"Institute for Medical Informatics and Biostatistics","ror":"https://ror.org/04e79zk25","country_code":"CH","type":"facility","lineage":["https://openalex.org/I4210163477"]}],"countries":["CH","US"],"is_corresponding":false,"raw_author_name":"Yuqing Wu","raw_affiliation_strings":["Center for Translational Bioinformatics, Washington University School of Medicine , St. Louis, MO,","Institute for Informatics, Data Science and Biostatistics, Washington University School of Medicine , Saint Louis, MO,","McDonnell Genome Institute, Washington University School of Medicine , St. Louis, MO,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Translational Bioinformatics, Washington University School of Medicine , St. Louis, MO,","institution_ids":["https://openalex.org/I204465549"]},{"raw_affiliation_string":"Institute for Informatics, Data Science and Biostatistics, Washington University School of Medicine , Saint Louis, MO,","institution_ids":["https://openalex.org/I4210163477"]},{"raw_affiliation_string":"McDonnell Genome Institute, Washington University School of Medicine , St. Louis, MO,","institution_ids":["https://openalex.org/I114277686"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5102730779","display_name":"Yidan Sun","orcid":"https://orcid.org/0000-0003-4019-8077"},"institutions":[{"id":"https://openalex.org/I114277686","display_name":"James S. McDonnell Foundation","ror":"https://ror.org/03dy4aq19","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I114277686"]},{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]},{"id":"https://openalex.org/I4210163477","display_name":"Institute for Medical Informatics and Biostatistics","ror":"https://ror.org/04e79zk25","country_code":"CH","type":"facility","lineage":["https://openalex.org/I4210163477"]}],"countries":["CH","US"],"is_corresponding":false,"raw_author_name":"Yidan Sun","raw_affiliation_strings":["Center for Translational Bioinformatics, Washington University School of Medicine , St. Louis, MO,","Department of Genetics, Washington University School of Medicine , St. Louis, MO,","Institute for Informatics, Data Science and Biostatistics, Washington University School of Medicine , Saint Louis, MO,","McDonnell Genome Institute, Washington University School of Medicine , St. Louis, MO,"],"raw_orcid":"https://orcid.org/0000-0003-4019-8077","affiliations":[{"raw_affiliation_string":"Center for Translational Bioinformatics, Washington University School of Medicine , St. Louis, MO,","institution_ids":["https://openalex.org/I204465549"]},{"raw_affiliation_string":"Department of Genetics, Washington University School of Medicine , St. Louis, MO,","institution_ids":["https://openalex.org/I204465549"]},{"raw_affiliation_string":"Institute for Informatics, Data Science and Biostatistics, Washington University School of Medicine , Saint Louis, MO,","institution_ids":["https://openalex.org/I4210163477"]},{"raw_affiliation_string":"McDonnell Genome Institute, Washington University School of Medicine , St. Louis, MO,","institution_ids":["https://openalex.org/I114277686"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"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":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.82312925,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"42","issue":"8","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.7247999906539917,"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/T10604","display_name":"RNA Research and Splicing","score":0.7247999906539917,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.07109999656677246,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.0608999989926815,"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/pipeline","display_name":"Pipeline (software)","score":0.6363999843597412},{"id":"https://openalex.org/keywords/nanopore-sequencing","display_name":"Nanopore sequencing","score":0.593500018119812},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5321000218391418},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.5192999839782715},{"id":"https://openalex.org/keywords/limiting","display_name":"Limiting","score":0.5041000247001648},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.49729999899864197},{"id":"https://openalex.org/keywords/transposable-element","display_name":"Transposable element","score":0.4586000144481659},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.3905999958515167}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6589999794960022},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6363999843597412},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6111999750137329},{"id":"https://openalex.org/C126513998","wikidata":"https://www.wikidata.org/wiki/Q8973627","display_name":"Nanopore sequencing","level":4,"score":0.593500018119812},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5321000218391418},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.5192999839782715},{"id":"https://openalex.org/C188198153","wikidata":"https://www.wikidata.org/wiki/Q1613840","display_name":"Limiting","level":2,"score":0.5041000247001648},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.49729999899864197},{"id":"https://openalex.org/C4918238","wikidata":"https://www.wikidata.org/wiki/Q121438","display_name":"Transposable element","level":4,"score":0.4586000144481659},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3961000144481659},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.3905999958515167},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.38920000195503235},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3111000061035156},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3068999946117401},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.30160000920295715},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.2962000072002411},{"id":"https://openalex.org/C21592294","wikidata":"https://www.wikidata.org/wiki/Q3238407","display_name":"Regulatory sequence","level":4,"score":0.27480000257492065},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2606000006198883},{"id":"https://openalex.org/C2776207758","wikidata":"https://www.wikidata.org/wiki/Q5303302","display_name":"Downstream (manufacturing)","level":2,"score":0.25949999690055847},{"id":"https://openalex.org/C61053724","wikidata":"https://www.wikidata.org/wiki/Q1154615","display_name":"Sequence analysis","level":3,"score":0.2574999928474426},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.2574000060558319},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.25589999556541443},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.25099998712539673}],"mesh":[{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btag518","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag518","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:42544764","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42544764","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":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:13439700","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13439700/","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/btag518","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag518","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":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":21,"referenced_works":["https://openalex.org/W2179438025","https://openalex.org/W2275033707","https://openalex.org/W2341539131","https://openalex.org/W2432815617","https://openalex.org/W2775755225","https://openalex.org/W2789843538","https://openalex.org/W2949317881","https://openalex.org/W2949324846","https://openalex.org/W2954932330","https://openalex.org/W2971958993","https://openalex.org/W3006653136","https://openalex.org/W3007172120","https://openalex.org/W3011428862","https://openalex.org/W4234344490","https://openalex.org/W4313454274","https://openalex.org/W4360752233","https://openalex.org/W4360999762","https://openalex.org/W4380319111","https://openalex.org/W4399437507","https://openalex.org/W4408936761","https://openalex.org/W7128202531"],"related_works":[],"abstract_inverted_index":{"SUMMARY:":[0],"Long-read":[1],"RNA":[2],"sequencing":[3],"technologies,":[4],"including":[5],"Pacific":[6],"Biosciences":[7],"(PacBio)":[8],"and":[9,20,46,57,99,101,108,140,147],"Oxford":[10],"Nanopore":[11],"Technologies":[12],"(ONT),":[13],"enable":[14],"direct":[15],"characterization":[16],"of":[17,25,42,65,68,129],"full-length":[18],"transcripts":[19],"transcriptome":[21],"complexity.":[22],"However,":[23],"analysis":[24,64],"long-read":[26,50],"RNA-seq":[27],"data":[28,115],"remains":[29],"fragmented":[30],"across":[31],"multiple":[32,66],"tools,":[33],"limiting":[34],"the":[35,121],"ability":[36],"to":[37,86,126],"obtain":[38],"a":[39,55],"unified":[40,118],"view":[41],"transcript":[43,69,76,80,93,124],"structure,":[44],"expression,":[45],"regulatory":[47,84],"variation":[48],"in":[49,138],"transcriptomes.":[51],"We":[52],"present":[53],"NextLongIso,":[54],"scalable":[56],"reproducible":[58],"Nextflow":[59,139],"pipeline":[60],"that":[61],"enables":[62],"coordinated":[63],"layers":[67],"regulation.":[70],"Rather":[71],"than":[72],"focusing":[73],"solely":[74],"on":[75],"reconstruction,":[77],"NextLongIso":[78,135],"integrates":[79],"discovery":[81],"with":[82],"downstream":[83],"analyses":[85],"jointly":[87],"characterize":[88],"alternative":[89,97],"splicing,":[90],"isoform":[91],"switching,":[92],"boundary":[94],"dynamics":[95],"(including":[96],"promoters":[98],"polyadenylation),":[100],"transposable":[102],"element-associated":[103],"transcription":[104],"from":[105,123],"both":[106],"PacBio":[107],"ONT":[109],"datasets.":[110],"By":[111],"eliminating":[112],"complex":[113],"cross-tool":[114],"harmonization,":[116],"this":[117],"framework":[119],"facilitates":[120],"transition":[122],"identification":[125],"functional":[127],"interpretation":[128],"transcriptomic":[130],"variation.":[131],"AVAILABILITY":[132],"AND":[133],"IMPLEMENTATION:":[134],"is":[136,141],"implemented":[137],"freely":[142],"available":[143],"at":[144],"github:":[145],"https://github.com/YidanSunResearchLab/nf-LongIso.git":[146],"Zenodo:":[148],"https://doi.org/10.5281/zenodo.21049837.":[149]},"counts_by_year":[],"updated_date":"2026-08-08T07:41:36.138363","created_date":"2026-08-04T00:00:00"}
