{"id":"https://openalex.org/W2415325177","doi":"https://doi.org/10.1186/s12859-016-1104-8","title":"SUSHI: an exquisite recipe for fully documented, reproducible and reusable NGS data analysis","display_name":"SUSHI: an exquisite recipe for fully documented, reproducible and reusable NGS data analysis","publication_year":2016,"publication_date":"2016-06-02","ids":{"openalex":"https://openalex.org/W2415325177","doi":"https://doi.org/10.1186/s12859-016-1104-8","mag":"2415325177","pmid":"https://pubmed.ncbi.nlm.nih.gov/27255077"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-016-1104-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-016-1104-8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-016-1104-8","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-016-1104-8","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5084265053","display_name":"Masaomi Hatakeyama","orcid":"https://orcid.org/0000-0002-7409-9694"},"institutions":[{"id":"https://openalex.org/I200744771","display_name":"ZHAW Zurich University of Applied Sciences","ror":null,"country_code":"CH","type":null,"lineage":["https://openalex.org/I200744771"]},{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]},{"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"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Masaomi Hatakeyama","raw_affiliation_strings":["Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse. 190, 8057, Zurich, Switzerland","Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Winterthurerstrasse. 190, 8057, Zurich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse. 190, 8057, Zurich, Switzerland","institution_ids":["https://openalex.org/I200744771","https://openalex.org/I202697423"]},{"raw_affiliation_string":"Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Winterthurerstrasse. 190, 8057, Zurich, Switzerland","institution_ids":["https://openalex.org/I202697423","https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055753996","display_name":"Lennart Opitz","orcid":"https://orcid.org/0000-0001-7945-6737"},"institutions":[{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]},{"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"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Lennart Opitz","raw_affiliation_strings":["Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Winterthurerstrasse. 190, 8057, Zurich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Winterthurerstrasse. 190, 8057, Zurich, Switzerland","institution_ids":["https://openalex.org/I202697423","https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010185305","display_name":"Giancarlo Russo","orcid":"https://orcid.org/0000-0003-0707-2640"},"institutions":[{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]},{"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"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Giancarlo Russo","raw_affiliation_strings":["Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Winterthurerstrasse. 190, 8057, Zurich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Winterthurerstrasse. 190, 8057, Zurich, Switzerland","institution_ids":["https://openalex.org/I202697423","https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089938252","display_name":"Weihong Qi","orcid":"https://orcid.org/0000-0001-8581-908X"},"institutions":[{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]},{"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"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Weihong Qi","raw_affiliation_strings":["Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Winterthurerstrasse. 190, 8057, Zurich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Winterthurerstrasse. 190, 8057, Zurich, Switzerland","institution_ids":["https://openalex.org/I202697423","https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037036136","display_name":"Ralph Schlapbach","orcid":"https://orcid.org/0000-0002-7488-4262"},"institutions":[{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]},{"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"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Ralph Schlapbach","raw_affiliation_strings":["Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Winterthurerstrasse. 190, 8057, Zurich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Winterthurerstrasse. 190, 8057, Zurich, Switzerland","institution_ids":["https://openalex.org/I202697423","https://openalex.org/I35440088"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5005269336","display_name":"Hubert Rehrauer","orcid":"https://orcid.org/0000-0001-7612-9394"},"institutions":[{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]},{"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"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Hubert Rehrauer","raw_affiliation_strings":["Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Winterthurerstrasse. 190, 8057, Zurich, Switzerland. hubert.rehrauer@fgcz.ethz.ch","Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Winterthurerstrasse. 190, 8057, Zurich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Winterthurerstrasse. 190, 8057, Zurich, Switzerland. hubert.rehrauer@fgcz.ethz.ch","institution_ids":["https://openalex.org/I35440088","https://openalex.org/I202697423"]},{"raw_affiliation_string":"Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Winterthurerstrasse. 190, 8057, Zurich, Switzerland","institution_ids":["https://openalex.org/I202697423","https://openalex.org/I35440088"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5084265053"],"corresponding_institution_ids":["https://openalex.org/I200744771","https://openalex.org/I202697423","https://openalex.org/I35440088"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":18.9538,"has_fulltext":true,"cited_by_count":147,"citation_normalized_percentile":{"value":0.98895508,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"17","issue":"1","first_page":"228","last_page":"228"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.4593999981880188,"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":0.4593999981880188,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.2865999937057495,"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":0.07360000163316727,"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":0.7818045616149902},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.6702226400375366},{"id":"https://openalex.org/keywords/scripting-language","display_name":"Scripting language","score":0.6493860483169556},{"id":"https://openalex.org/keywords/recipe","display_name":"Recipe","score":0.5936780571937561},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.5580883026123047},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.5296518802642822},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.522922158241272},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.46195530891418457},{"id":"https://openalex.org/keywords/automatic-summarization","display_name":"Automatic summarization","score":0.43576741218566895},{"id":"https://openalex.org/keywords/web-application","display_name":"Web application","score":0.4189724624156952},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.38069218397140503},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.2562008500099182},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.11650970578193665}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7818045616149902},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.6702226400375366},{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.6493860483169556},{"id":"https://openalex.org/C2778671685","wikidata":"https://www.wikidata.org/wiki/Q219239","display_name":"Recipe","level":2,"score":0.5936780571937561},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.5580883026123047},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.5296518802642822},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.522922158241272},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.46195530891418457},{"id":"https://openalex.org/C170858558","wikidata":"https://www.wikidata.org/wiki/Q1394144","display_name":"Automatic summarization","level":2,"score":0.43576741218566895},{"id":"https://openalex.org/C118643609","wikidata":"https://www.wikidata.org/wiki/Q189210","display_name":"Web application","level":2,"score":0.4189724624156952},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.38069218397140503},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.2562008500099182},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.11650970578193665},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.0},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"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/C31903555","wikidata":"https://www.wikidata.org/wiki/Q1637030","display_name":"Food science","level":1,"score":0.0}],"mesh":[{"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":"D013223","descriptor_name":"Statistics as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013223","descriptor_name":"Statistics as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013223","descriptor_name":"Statistics as Topic","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","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},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1186/s12859-016-1104-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-016-1104-8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-016-1104-8","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:27255077","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27255077","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:www.zora.uzh.ch:131257","is_oa":true,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306401281","display_name":"Zurich Open Repository and Archive (University of Zurich)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I202697423","host_organization_name":"University of Zurich","host_organization_lineage":["https://openalex.org/I202697423"],"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":"Hatakeyama, Masaomi; Opitz, Lennart; Russo, Giancarlo; Qi, Weihong; Schlapbach, Ralph; Rehrauer, Hubert  (2016). SUSHI: an exquisite recipe for fully documented, reproducible and reusable NGS data analysis.  BMC Bioinformatics, 17(1):228.","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:pubmedcentral.nih.gov:4890512","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4890512","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":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:www.research-collection.ethz.ch:20.500.11850/117457","is_oa":true,"landing_page_url":"http://hdl.handle.net/20.500.11850/117457","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, 17","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"doi:10.3929/ethz-b-000117457","is_oa":true,"landing_page_url":"https://doi.org/10.3929/ethz-b-000117457","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"},{"id":"doi:10.5167/uzh-131257","is_oa":true,"landing_page_url":"https://doi.org/10.5167/uzh-131257","pdf_url":null,"source":{"id":"https://openalex.org/S7407051291","display_name":"Universit\u00e4t Z\u00fcrich, ZORA","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:10.1186/s12859-016-1104-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-016-1104-8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-016-1104-8","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Decent work and economic growth","id":"https://metadata.un.org/sdg/8","score":0.4699999988079071}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2415325177.pdf","grobid_xml":"https://content.openalex.org/works/W2415325177.grobid-xml"},"referenced_works_count":29,"referenced_works":["https://openalex.org/W952303715","https://openalex.org/W1525509699","https://openalex.org/W1535654799","https://openalex.org/W1556533941","https://openalex.org/W1759083992","https://openalex.org/W1977859620","https://openalex.org/W1996345933","https://openalex.org/W2013434113","https://openalex.org/W2030955639","https://openalex.org/W2096525273","https://openalex.org/W2097438318","https://openalex.org/W2106831214","https://openalex.org/W2110417468","https://openalex.org/W2110905563","https://openalex.org/W2114104545","https://openalex.org/W2118258530","https://openalex.org/W2119298573","https://openalex.org/W2122772178","https://openalex.org/W2123100726","https://openalex.org/W2123828642","https://openalex.org/W2124796057","https://openalex.org/W2136482257","https://openalex.org/W2140503409","https://openalex.org/W2140729960","https://openalex.org/W2141297584","https://openalex.org/W2169456326","https://openalex.org/W2172194140","https://openalex.org/W2335932981","https://openalex.org/W4251386234"],"related_works":["https://openalex.org/W258429745","https://openalex.org/W3161239248","https://openalex.org/W2561508161","https://openalex.org/W3195543079","https://openalex.org/W2098178683","https://openalex.org/W3207562294","https://openalex.org/W2604742737","https://openalex.org/W3021194804","https://openalex.org/W4386893202","https://openalex.org/W1486385073"],"abstract_inverted_index":{"BACKGROUND:":[0],"Next":[1],"generation":[2],"sequencing":[3],"(NGS)":[4],"produces":[5],"massive":[6],"datasets":[7,135,165],"consisting":[8],"of":[9,11,17,28,83,198],"billions":[10],"reads":[12],"and":[13,59,64,98,109,138,149,171,195,200,248],"up":[14],"to":[15,51,130,151,211],"thousands":[16],"samples.":[18],"Subsequent":[19],"bioinformatic":[20],"analysis":[21,74,93,193,213,253,260],"is":[22,216,229,244],"typically":[23],"done":[24],"with":[25,48,106],"the":[26,40,46,49,53,56,62,80,100,103,110,141,155,164,187,204,212],"help":[27],"open":[29],"source":[30,263],"tools,":[31,54],"where":[32],"each":[33],"application":[34],"performs":[35],"a":[36,126,268],"single":[37],"step":[38],"towards":[39],"final":[41],"result.":[42],"This":[43,144],"situation":[44],"leaves":[45],"bioinformaticians":[47,78,221],"tasks":[50],"combine":[52],"manage":[55],"data":[57,73,85,92,192,239,252,259],"files":[58],"meta-information,":[60],"document":[61],"analysis,":[63],"ensure":[65],"reproducibility.":[66],"RESULTS:":[67],"We":[68],"present":[69],"SUSHI,":[70],"an":[71,118,178],"agile":[72],"framework":[75],"that":[76],"relieves":[77],"from":[79,95],"administrative":[81],"challenges":[82],"their":[84],"analysis.":[86,240],"SUSHI":[87,116,134,176,188,190,215,242,262],"lets":[88],"users":[89],"build":[90],"reproducible":[91,148],"workflows":[94],"individual":[96],"applications":[97],"manages":[99],"input":[101],"data,":[102],"parameters,":[104],"meta-information":[105,157],"user-driven":[107],"semantics,":[108],"job":[111],"scripts.":[112],"As":[113],"distinguishing":[114],"features,":[115],"provides":[117,177],"expert":[119],"command":[120],"line":[121],"interface":[122,129,254],"as":[123,125,160,222,224,251,265,267],"well":[124,223,266],"convenient":[127],"web":[128],"run":[131],"bioinformatics":[132],"tools.":[133],"are":[136,271],"self-contained":[137],"self-documented":[139],"on":[140],"file":[142],"system.":[143],"makes":[145,191],"them":[146],"fully":[147,207],"ready":[150],"be":[152,167],"shared.":[153],"With":[154],"associated":[156],"being":[158],"formatted":[159],"plain":[161],"text":[162],"tables,":[163],"can":[166,206],"readily":[168],"further":[169],"analyzed":[170],"interpreted":[172],"outside":[173],"SUSHI.":[174],"CONCLUSION:":[175],"exquisite":[179],"recipe":[180],"for":[181,218,255],"analysing":[182],"NGS":[183,238],"data.":[184],"By":[185],"following":[186],"recipe,":[189],"straightforward":[194],"takes":[196],"care":[197],"documentation":[199],"administration":[201],"tasks.":[202],"Thus,":[203],"user":[205],"dedicate":[208],"his":[209],"time":[210],"itself.":[214],"suitable":[217],"use":[219,247],"by":[220,233],"life":[225],"science":[226],"researchers.":[227],"It":[228],"targeted":[230],"for,":[231],"but":[232],"no":[234],"means":[235],"constrained":[236],"to,":[237],"Our":[241],"instance":[243],"in":[245],"productive":[246],"has":[249],"served":[250],"more":[256],"than":[257],"1000":[258],"projects.":[261],"code":[264],"demo":[269],"server":[270],"freely":[272],"available.":[273]},"counts_by_year":[{"year":2026,"cited_by_count":11},{"year":2025,"cited_by_count":22},{"year":2024,"cited_by_count":20},{"year":2023,"cited_by_count":19},{"year":2022,"cited_by_count":18},{"year":2021,"cited_by_count":23},{"year":2020,"cited_by_count":14},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":7},{"year":2016,"cited_by_count":1}],"updated_date":"2026-05-05T08:41:31.759640","created_date":"2025-10-10T00:00:00"}