{"id":"https://openalex.org/W4282823156","doi":"https://doi.org/10.1093/bioinformatics/btac389","title":"SNIKT: sequence-independent adapter identification and removal in long-read shotgun sequencing data","display_name":"SNIKT: sequence-independent adapter identification and removal in long-read shotgun sequencing data","publication_year":2022,"publication_date":"2022-06-13","ids":{"openalex":"https://openalex.org/W4282823156","doi":"https://doi.org/10.1093/bioinformatics/btac389","pmid":"https://pubmed.ncbi.nlm.nih.gov/35695743"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac389","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac389","pdf_url":null,"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":null,"license_id":null,"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":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9991892","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5075582506","display_name":"Piyush Ranjan","orcid":"https://orcid.org/0000-0001-8293-6889"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Piyush Ranjan","raw_affiliation_strings":["Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School , Ann Arbor, MI 48109, USA"],"affiliations":[{"raw_affiliation_string":"Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School , Ann Arbor, MI 48109, USA","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101620637","display_name":"Christopher A. Brown","orcid":"https://orcid.org/0000-0001-8855-4355"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christopher A Brown","raw_affiliation_strings":["Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School , Ann Arbor, MI 48109, USA","Institute for Research on Innovation and Science, Institute for Social Research, University of Michigan , Ann Arbor, MI 48109, USA"],"affiliations":[{"raw_affiliation_string":"Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School , Ann Arbor, MI 48109, USA","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"Institute for Research on Innovation and Science, Institute for Social Research, University of Michigan , Ann Arbor, MI 48109, USA","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062465162","display_name":"John R. Erb\u2010Downward","orcid":"https://orcid.org/0000-0002-4233-758X"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John R Erb-Downward","raw_affiliation_strings":["Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School , Ann Arbor, MI 48109, USA"],"affiliations":[{"raw_affiliation_string":"Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School , Ann Arbor, MI 48109, USA","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5060487785","display_name":"Robert P. Dickson","orcid":"https://orcid.org/0000-0002-6875-4277"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]},{"id":"https://openalex.org/I4210140958","display_name":"Ann Arbor Center for Independent Living","ror":"https://ror.org/045pcya52","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210140958"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert P Dickson","raw_affiliation_strings":["Department of Microbiology and Immunology, University of Michigan Medical School , Ann Arbor, MI 48109, USA","Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School , Ann Arbor, MI 48109, USA","Weil Institute for Critical Care Research & Innovation , Ann Arbor, MI 48109, USA"],"affiliations":[{"raw_affiliation_string":"Department of Microbiology and Immunology, University of Michigan Medical School , Ann Arbor, MI 48109, USA","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School , Ann Arbor, MI 48109, USA","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"Weil Institute for Critical Care Research & Innovation , Ann Arbor, MI 48109, USA","institution_ids":["https://openalex.org/I4210140958"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5075582506"],"corresponding_institution_ids":["https://openalex.org/I27837315"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.434,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.5819095,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"38","issue":"15","first_page":"3830","last_page":"3832"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998999834060669,"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":0.9998999834060669,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9962999820709229,"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/T12640","display_name":"Environmental DNA in Biodiversity Studies","score":0.9958999752998352,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/adapter","display_name":"Adapter (computing)","score":0.9405732154846191},{"id":"https://openalex.org/keywords/shotgun","display_name":"Shotgun","score":0.7432657480239868},{"id":"https://openalex.org/keywords/shotgun-sequencing","display_name":"Shotgun sequencing","score":0.7347047328948975},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6577762961387634},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.6537870764732361},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.568405270576477},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.5455223917961121},{"id":"https://openalex.org/keywords/unix","display_name":"Unix","score":0.4755432605743408},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4510079622268677},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.43702441453933716},{"id":"https://openalex.org/keywords/sequence-assembly","display_name":"Sequence assembly","score":0.4150502681732178},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.369388610124588},{"id":"https://openalex.org/keywords/license","display_name":"License","score":0.36503416299819946},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3402935266494751},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.329314649105072},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.277164101600647},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.24970069527626038},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2299814224243164},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.1934586465358734},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.14590981602668762},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11094418168067932}],"concepts":[{"id":"https://openalex.org/C177284502","wikidata":"https://www.wikidata.org/wiki/Q1005390","display_name":"Adapter (computing)","level":2,"score":0.9405732154846191},{"id":"https://openalex.org/C2781434637","wikidata":"https://www.wikidata.org/wiki/Q486396","display_name":"Shotgun","level":3,"score":0.7432657480239868},{"id":"https://openalex.org/C101985253","wikidata":"https://www.wikidata.org/wiki/Q1073526","display_name":"Shotgun sequencing","level":4,"score":0.7347047328948975},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6577762961387634},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.6537870764732361},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.568405270576477},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.5455223917961121},{"id":"https://openalex.org/C112968700","wikidata":"https://www.wikidata.org/wiki/Q11368","display_name":"Unix","level":3,"score":0.4755432605743408},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4510079622268677},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.43702441453933716},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.4150502681732178},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.369388610124588},{"id":"https://openalex.org/C2780560020","wikidata":"https://www.wikidata.org/wiki/Q79719","display_name":"License","level":2,"score":0.36503416299819946},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3402935266494751},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.329314649105072},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.277164101600647},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.24970069527626038},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2299814224243164},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.1934586465358734},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.14590981602668762},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11094418168067932},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btac389","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac389","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35695743","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35695743","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:9991892","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9991892","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:9991892","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9991892","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4730717215","display_name":null,"funder_award_id":"T32HL007749","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4974824887","display_name":null,"funder_award_id":"R01HL144599","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"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/W2036897871","https://openalex.org/W2131271579","https://openalex.org/W2139436361","https://openalex.org/W2550586733","https://openalex.org/W2758005814","https://openalex.org/W2765745983","https://openalex.org/W2801006204","https://openalex.org/W2898604559","https://openalex.org/W2951278111","https://openalex.org/W2990427812","https://openalex.org/W3172076548","https://openalex.org/W4399540501"],"related_works":["https://openalex.org/W4210312276","https://openalex.org/W2417514914","https://openalex.org/W1641084016","https://openalex.org/W2018832993","https://openalex.org/W4255415692","https://openalex.org/W3128701120","https://openalex.org/W2733238538","https://openalex.org/W2741645994","https://openalex.org/W4282823156","https://openalex.org/W2147623421"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":1}],"updated_date":"2026-04-07T14:57:38.498316","created_date":"2025-10-10T00:00:00"}
