{"id":"https://openalex.org/W7131260688","doi":"https://doi.org/10.1093/bioinformatics/btag097","title":"RUMINA: high-throughput deduplication of unique molecular identifiers for amplicon and whole-genome sequencing with enhanced error correction","display_name":"RUMINA: high-throughput deduplication of unique molecular identifiers for amplicon and whole-genome sequencing with enhanced error correction","publication_year":2026,"publication_date":"2026-02-24","ids":{"openalex":"https://openalex.org/W7131260688","doi":"https://doi.org/10.1093/bioinformatics/btag097","pmid":"https://pubmed.ncbi.nlm.nih.gov/41734278"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btag097","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag097","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/btag097","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5093435405","display_name":"Eli A. Piliper","orcid":"https://orcid.org/0009-0005-9278-3907"},"institutions":[{"id":"https://openalex.org/I2801852214","display_name":"University of Washington Medical Center","ror":"https://ror.org/00wbzw723","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2801852214"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Eli Piliper","raw_affiliation_strings":["Department of Laboratory Medicine and Pathology, University of Washington Medical Center , Seattle, 98109, Washington,"],"affiliations":[{"raw_affiliation_string":"Department of Laboratory Medicine and Pathology, University of Washington Medical Center , Seattle, 98109, Washington,","institution_ids":["https://openalex.org/I2801852214"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5106941660","display_name":"Stephanie Goya","orcid":"https://orcid.org/0000-0001-7479-3064"},"institutions":[{"id":"https://openalex.org/I2801852214","display_name":"University of Washington Medical Center","ror":"https://ror.org/00wbzw723","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2801852214"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Stephanie Goya","raw_affiliation_strings":["Department of Laboratory Medicine and Pathology, University of Washington Medical Center , Seattle, 98109, Washington,"],"affiliations":[{"raw_affiliation_string":"Department of Laboratory Medicine and Pathology, University of Washington Medical Center , Seattle, 98109, Washington,","institution_ids":["https://openalex.org/I2801852214"]}]},{"author_position":"last","author":{"id":null,"display_name":"Alexander L Greninger","orcid":"https://orcid.org/0000-0002-7443-0527"},"institutions":[{"id":"https://openalex.org/I1330732676","display_name":"Infectious Disease Research Institute","ror":"https://ror.org/03y4myd35","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1330732676"]},{"id":"https://openalex.org/I2801852214","display_name":"University of Washington Medical Center","ror":"https://ror.org/00wbzw723","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2801852214"]},{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alexander L Greninger","raw_affiliation_strings":["Department of Laboratory Medicine and Pathology, University of Washington Medical Center , Seattle, 98109, Washington,","Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center , Seattle, 98109, Washington,"],"affiliations":[{"raw_affiliation_string":"Department of Laboratory Medicine and Pathology, University of Washington Medical Center , Seattle, 98109, Washington,","institution_ids":["https://openalex.org/I2801852214"]},{"raw_affiliation_string":"Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center , Seattle, 98109, Washington,","institution_ids":["https://openalex.org/I4210089486","https://openalex.org/I1330732676"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5093435405"],"corresponding_institution_ids":["https://openalex.org/I2801852214"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.63864032,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"42","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.8187999725341797,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.8187999725341797,"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/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.04780000075697899,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.0340999998152256,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/data-deduplication","display_name":"Data deduplication","score":0.8567000031471252},{"id":"https://openalex.org/keywords/amplicon","display_name":"Amplicon","score":0.670199990272522},{"id":"https://openalex.org/keywords/error-detection-and-correction","display_name":"Error detection and correction","score":0.6592000126838684},{"id":"https://openalex.org/keywords/amplicon-sequencing","display_name":"Amplicon sequencing","score":0.4007999897003174},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.3587000072002411},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.32170000672340393}],"concepts":[{"id":"https://openalex.org/C32587265","wikidata":"https://www.wikidata.org/wiki/Q1182260","display_name":"Data deduplication","level":2,"score":0.8567000031471252},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7601000070571899},{"id":"https://openalex.org/C8185291","wikidata":"https://www.wikidata.org/wiki/Q2844457","display_name":"Amplicon","level":4,"score":0.670199990272522},{"id":"https://openalex.org/C103088060","wikidata":"https://www.wikidata.org/wiki/Q1062839","display_name":"Error detection and correction","level":2,"score":0.6592000126838684},{"id":"https://openalex.org/C2993206177","wikidata":"https://www.wikidata.org/wiki/Q2844457","display_name":"Amplicon sequencing","level":4,"score":0.4007999897003174},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.37290000915527344},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3686999976634979},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.3587000072002411},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3386000096797943},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3359000086784363},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.32170000672340393},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.31119999289512634},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.2924000024795532},{"id":"https://openalex.org/C3018824978","wikidata":"https://www.wikidata.org/wiki/Q2894891","display_name":"Error analysis","level":2,"score":0.2838999927043915},{"id":"https://openalex.org/C2984717058","wikidata":"https://www.wikidata.org/wiki/Q1789476","display_name":"Reference database","level":2,"score":0.2535000145435333}],"mesh":[{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","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":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","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":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btag097","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag097","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:41734278","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41734278","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:12975283","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12975283/","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btag097","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag097","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":[{"id":"https://openalex.org/F4320310094","display_name":"University of Washington","ror":"https://ror.org/00cvxb145"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":12,"referenced_works":["https://openalex.org/W2041677964","https://openalex.org/W2235876070","https://openalex.org/W2291938858","https://openalex.org/W2790798048","https://openalex.org/W2952109315","https://openalex.org/W2981107258","https://openalex.org/W2996575833","https://openalex.org/W3115496777","https://openalex.org/W3134736266","https://openalex.org/W3148807116","https://openalex.org/W4319299460","https://openalex.org/W4403253590"],"related_works":[],"abstract_inverted_index":{"RUMINA":[0],"is":[1,27],"implemented":[2],"in":[3],"Rust":[4],"and":[5,10,15],"distributed":[6],"as":[7],"open-source":[8],"code":[9,14],"precompiled":[11],"binaries.":[12],"Source":[13],"installation":[16],"instructions":[17],"are":[18],"available":[19,28],"at":[20,29],"https://github.com/greninger-lab/rumina.":[21],"Documentation":[22],"associated":[23],"with":[24],"this":[25],"manuscript":[26],"https://github.com/greninger-lab/rumina_paper.":[30]},"counts_by_year":[],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2026-02-25T00:00:00"}