{"id":"https://openalex.org/W2983726220","doi":"https://doi.org/10.1093/bioinformatics/btz850","title":"DigestiFlow: from BCL to FASTQ with ease","display_name":"DigestiFlow: from BCL to FASTQ with ease","publication_year":2019,"publication_date":"2019-11-13","ids":{"openalex":"https://openalex.org/W2983726220","doi":"https://doi.org/10.1093/bioinformatics/btz850","mag":"2983726220"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz850","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz850","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/6/1983/32915294/btz850.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":"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"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/36/6/1983/32915294/btz850.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5039159586","display_name":"Manuel Holtgrewe","orcid":"https://orcid.org/0000-0002-3051-1763"},"institutions":[{"id":"https://openalex.org/I4210139777","display_name":"Berlin Institute of Health at Charit\u00e9 - Universit\u00e4tsmedizin Berlin","ror":"https://ror.org/0493xsw21","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210139777","https://openalex.org/I7877124"]},{"id":"https://openalex.org/I7877124","display_name":"Charit\u00e9 - Universit\u00e4tsmedizin Berlin","ror":"https://ror.org/001w7jn25","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I7877124"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Manuel Holtgrewe","raw_affiliation_strings":["Charit\u00e9 \u2014 University Medicine Berlin , Berlin 10117, Germany","Core Unit Bioinformatics, Berlin Institute of Health , Berlin 10178, Germany"],"affiliations":[{"raw_affiliation_string":"Charit\u00e9 \u2014 University Medicine Berlin , Berlin 10117, Germany","institution_ids":["https://openalex.org/I7877124"]},{"raw_affiliation_string":"Core Unit Bioinformatics, Berlin Institute of Health , Berlin 10178, Germany","institution_ids":["https://openalex.org/I4210139777"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074141837","display_name":"Clemens Messerschmidt","orcid":"https://orcid.org/0000-0001-8632-656X"},"institutions":[{"id":"https://openalex.org/I4210139777","display_name":"Berlin Institute of Health at Charit\u00e9 - Universit\u00e4tsmedizin Berlin","ror":"https://ror.org/0493xsw21","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210139777","https://openalex.org/I7877124"]},{"id":"https://openalex.org/I7877124","display_name":"Charit\u00e9 - Universit\u00e4tsmedizin Berlin","ror":"https://ror.org/001w7jn25","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I7877124"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Clemens Messerschmidt","raw_affiliation_strings":["Charit\u00e9 \u2014 University Medicine Berlin , Berlin 10117, Germany","Core Unit Bioinformatics, Berlin Institute of Health , Berlin 10178, Germany"],"affiliations":[{"raw_affiliation_string":"Charit\u00e9 \u2014 University Medicine Berlin , Berlin 10117, Germany","institution_ids":["https://openalex.org/I7877124"]},{"raw_affiliation_string":"Core Unit Bioinformatics, Berlin Institute of Health , Berlin 10178, Germany","institution_ids":["https://openalex.org/I4210139777"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051299377","display_name":"Mikko Nieminen","orcid":"https://orcid.org/0000-0002-4180-8810"},"institutions":[{"id":"https://openalex.org/I205582932","display_name":"Max Delbr\u00fcck Center","ror":"https://ror.org/04p5ggc03","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I205582932"]},{"id":"https://openalex.org/I7877124","display_name":"Charit\u00e9 - Universit\u00e4tsmedizin Berlin","ror":"https://ror.org/001w7jn25","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I7877124"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Mikko Nieminen","raw_affiliation_strings":["Charit\u00e9 \u2014 University Medicine Berlin , Berlin 10117, Germany","Max Delbr\u00fcck Center for Molecular Medicine in the Helmholtz Association , Berlin 13125, Germany"],"affiliations":[{"raw_affiliation_string":"Charit\u00e9 \u2014 University Medicine Berlin , Berlin 10117, Germany","institution_ids":["https://openalex.org/I7877124"]},{"raw_affiliation_string":"Max Delbr\u00fcck Center for Molecular Medicine in the Helmholtz Association , Berlin 13125, Germany","institution_ids":["https://openalex.org/I205582932"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064391109","display_name":"Dieter Beule","orcid":"https://orcid.org/0000-0002-3284-0632"},"institutions":[{"id":"https://openalex.org/I205582932","display_name":"Max Delbr\u00fcck Center","ror":"https://ror.org/04p5ggc03","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I205582932"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Dieter Beule","raw_affiliation_strings":["Max Delbr\u00fcck Center for Molecular Medicine in the Helmholtz Association , Berlin 13125, Germany"],"affiliations":[{"raw_affiliation_string":"Max Delbr\u00fcck Center for Molecular Medicine in the Helmholtz Association , Berlin 13125, Germany","institution_ids":["https://openalex.org/I205582932"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5039159586"],"corresponding_institution_ids":["https://openalex.org/I4210139777","https://openalex.org/I7877124"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":1418,"currency":"EUR","value_usd":1529},"fwci":0.4403,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.83341212,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"36","issue":"6","first_page":"1983","last_page":"1985"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9986000061035156,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},"topics":[{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9986000061035156,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9932000041007996,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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":0.9846000075340271,"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/computer-science","display_name":"Computer science","score":0.812348484992981},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.7010962963104248},{"id":"https://openalex.org/keywords/raw-data","display_name":"Raw data","score":0.608999490737915},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.49880123138427734},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.48053106665611267},{"id":"https://openalex.org/keywords/sample","display_name":"Sample (material)","score":0.4764973521232605},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.46973761916160583},{"id":"https://openalex.org/keywords/license","display_name":"License","score":0.46311154961586},{"id":"https://openalex.org/keywords/multiplexing","display_name":"Multiplexing","score":0.45060279965400696},{"id":"https://openalex.org/keywords/data-management","display_name":"Data management","score":0.4377817213535309},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.19661659002304077},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.10715839266777039}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.812348484992981},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.7010962963104248},{"id":"https://openalex.org/C132964779","wikidata":"https://www.wikidata.org/wiki/Q2110223","display_name":"Raw data","level":2,"score":0.608999490737915},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.49880123138427734},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.48053106665611267},{"id":"https://openalex.org/C198531522","wikidata":"https://www.wikidata.org/wiki/Q485146","display_name":"Sample (material)","level":2,"score":0.4764973521232605},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.46973761916160583},{"id":"https://openalex.org/C2780560020","wikidata":"https://www.wikidata.org/wiki/Q79719","display_name":"License","level":2,"score":0.46311154961586},{"id":"https://openalex.org/C19275194","wikidata":"https://www.wikidata.org/wiki/Q222903","display_name":"Multiplexing","level":2,"score":0.45060279965400696},{"id":"https://openalex.org/C1668388","wikidata":"https://www.wikidata.org/wiki/Q1149776","display_name":"Data management","level":2,"score":0.4377817213535309},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.19661659002304077},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.10715839266777039},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btz850","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz850","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/6/1983/32915294/btz850.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":"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":"pmh:oai:pubmedcentral.nih.gov:7703778","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7703778","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btz850","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz850","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/6/1983/32915294/btz850.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.5199999809265137,"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320329666","display_name":"Berlin Institute of Health","ror":"https://ror.org/0493xsw21"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2983726220.pdf","grobid_xml":"https://content.openalex.org/works/W2983726220.grobid-xml"},"referenced_works_count":7,"referenced_works":["https://openalex.org/W2051668973","https://openalex.org/W2110417468","https://openalex.org/W2122344857","https://openalex.org/W2174655541","https://openalex.org/W2432815617","https://openalex.org/W2765745983","https://openalex.org/W2891106135"],"related_works":["https://openalex.org/W2036021480","https://openalex.org/W2546377002","https://openalex.org/W4285209474","https://openalex.org/W22571951","https://openalex.org/W2046541848","https://openalex.org/W4384009753","https://openalex.org/W2791776396","https://openalex.org/W4286531993","https://openalex.org/W2964820744","https://openalex.org/W4247858078"],"abstract_inverted_index":{"Abstract":[0],"Summary":[1],"Management":[2],"of":[3,36,69,83,91,103],"raw-sequencing":[4],"data":[5,88,148],"and":[6,12,30,41,75,89,100,109,115,125],"its":[7],"pre-processing":[8],"(conversion":[9],"into":[10],"sequences":[11,108],"demultiplexing)":[13],"remains":[14],"a":[15],"challenging":[16],"topic":[17],"for":[18,80,97],"groups":[19],"running":[20],"sequencing":[21,52],"devices.":[22],"They":[23],"face":[24],"many":[25],"challenges":[26],"in":[27],"such":[28],"efforts":[29],"solutions":[31],"ranging":[32],"from":[33,85],"manual":[34],"management":[35,45,68,90],"spreadsheets":[37],"to":[38,107],"very":[39],"complex":[40],"customized":[42],"laboratory":[43],"information":[44,84,146],"systems":[46],"handling":[47],"much":[48],"more":[49],"than":[50],"just":[51],"raw":[53,76],"data.":[54,77],"In":[55],"this":[56],"article,":[57],"we":[58],"describe":[59],"the":[60,67,98,110,132],"software":[61,128,139],"package":[62],"DigestiFlow":[63],"that":[64],"focuses":[65],"on":[66],"Illumina":[70,104],"flow":[71,86],"cell":[72,87],"sample":[73,92],"sheets":[74],"It":[78],"allows":[79,96],"automated":[81,99],"extraction":[82],"sheets.":[93],"Furthermore,":[94],"it":[95],"reproducible":[101],"conversion":[102],"base":[105],"calls":[106],"demultiplexing":[111],"thereof":[112],"using":[113],"bcl2fastq":[114],"Picard":[116],"Tools,":[117],"followed":[118],"by":[119],"quality":[120],"control":[121],"report":[122],"generation.":[123],"Availability":[124],"implementation":[126],"The":[127,137],"is":[129],"available":[130,142,150],"under":[131],"MIT":[133],"license":[134],"at":[135,151],"https://github.com/bihealth/digestiflow-server.":[136],"client":[138],"components":[140],"are":[141,149],"via":[143],"Bioconda.":[144],"Supplementary":[145,147],"Bioinformatics":[152],"online.":[153]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2020,"cited_by_count":1}],"updated_date":"2026-03-31T07:56:22.981413","created_date":"2025-10-10T00:00:00"}