{"id":"https://openalex.org/W2725252423","doi":"https://doi.org/10.21105/joss.00272","title":"khmer release v2.1: software for biological sequence analysis","display_name":"khmer release v2.1: software for biological sequence analysis","publication_year":2017,"publication_date":"2017-07-03","ids":{"openalex":"https://openalex.org/W2725252423","doi":"https://doi.org/10.21105/joss.00272","mag":"2725252423"},"language":"en","primary_location":{"id":"doi:10.21105/joss.00272","is_oa":true,"landing_page_url":"https://doi.org/10.21105/joss.00272","pdf_url":"https://joss.theoj.org/papers/10.21105/joss.00272.pdf","source":{"id":"https://openalex.org/S4210214273","display_name":"The Journal of Open Source Software","issn_l":"2475-9066","issn":["2475-9066"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315853","host_organization_name":"Open Journals","host_organization_lineage":["https://openalex.org/P4310315853"],"host_organization_lineage_names":["Open Journals"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The Journal of Open Source Software","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://joss.theoj.org/papers/10.21105/joss.00272.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5048840870","display_name":"Daniel Standage","orcid":null},"institutions":[{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Daniel Standage","raw_affiliation_strings":["Lab for Data Intensive Biology; School of Veterinary Medicine; University of California, Davis"],"affiliations":[{"raw_affiliation_string":"Lab for Data Intensive Biology; School of Veterinary Medicine; University of California, Davis","institution_ids":["https://openalex.org/I84218800"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102769266","display_name":"Ali Reza Yari","orcid":null},"institutions":[{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ali yari","raw_affiliation_strings":["Integrative Genetics and Genomics Graduate Group; University of California, Davis"],"affiliations":[{"raw_affiliation_string":"Integrative Genetics and Genomics Graduate Group; University of California, Davis","institution_ids":["https://openalex.org/I84218800"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112292657","display_name":"Lisa J. Cohen","orcid":null},"institutions":[{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lisa J. Cohen","raw_affiliation_strings":["Lab for Data Intensive Biology; School of Veterinary Medicine; University of California, Davis"],"affiliations":[{"raw_affiliation_string":"Lab for Data Intensive Biology; School of Veterinary Medicine; University of California, Davis","institution_ids":["https://openalex.org/I84218800"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020288899","display_name":"Michael R. Crusoe","orcid":"https://orcid.org/0000-0002-2961-9670"},"institutions":[{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael R. Crusoe","raw_affiliation_strings":["Department of Population Health and Reproduction; School of Veterinary Medicine; University of California, Davis","Computer Science Graduate Group; University of California, Davis","Molecular, Cellular, and Integrative Physiology Graduate Group; University of California, Davis"],"affiliations":[{"raw_affiliation_string":"Department of Population Health and Reproduction; School of Veterinary Medicine; University of California, Davis","institution_ids":["https://openalex.org/I84218800"]},{"raw_affiliation_string":"Computer Science Graduate Group; University of California, Davis","institution_ids":["https://openalex.org/I84218800"]},{"raw_affiliation_string":"Molecular, Cellular, and Integrative Physiology Graduate Group; University of California, Davis","institution_ids":["https://openalex.org/I84218800"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006335431","display_name":"T. Head","orcid":"https://orcid.org/0000-0003-0931-3698"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Tim Head","raw_affiliation_strings":["Wild Tree Tech"],"affiliations":[{"raw_affiliation_string":"Wild Tree Tech","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068533814","display_name":"Luiz Irber","orcid":"https://orcid.org/0000-0003-4371-9659"},"institutions":[{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Luiz Irber","raw_affiliation_strings":["Lab for Data Intensive Biology; School of Veterinary Medicine; University of California, Davis"],"affiliations":[{"raw_affiliation_string":"Lab for Data Intensive Biology; School of Veterinary Medicine; University of California, Davis","institution_ids":["https://openalex.org/I84218800"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054168199","display_name":"Shannon E K Joslin","orcid":null},"institutions":[{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shannon EK Joslin","raw_affiliation_strings":["Integrative Genetics and Genomics Graduate Group; University of California, Davis"],"affiliations":[{"raw_affiliation_string":"Integrative Genetics and Genomics Graduate Group; University of California, Davis","institution_ids":["https://openalex.org/I84218800"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003122511","display_name":"Nicole B. Kingsley","orcid":"https://orcid.org/0000-0001-8574-8592"},"institutions":[{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"N. B. Kingsley","raw_affiliation_strings":["Integrative Genetics and Genomics Graduate Group; University of California, Davis"],"affiliations":[{"raw_affiliation_string":"Integrative Genetics and Genomics Graduate Group; University of California, Davis","institution_ids":["https://openalex.org/I84218800"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078210447","display_name":"Kevin Murray","orcid":"https://orcid.org/0000-0002-2466-1917"},"institutions":[{"id":"https://openalex.org/I118347636","display_name":"Australian National University","ror":"https://ror.org/019wvm592","country_code":"AU","type":"education","lineage":["https://openalex.org/I118347636"]},{"id":"https://openalex.org/I4210102918","display_name":"ARC Centre of Excellence in Plant Energy Biology","ror":"https://ror.org/01a1mq059","country_code":"AU","type":"facility","lineage":["https://openalex.org/I118347636","https://openalex.org/I1337719021","https://openalex.org/I2801453606","https://openalex.org/I4210102918","https://openalex.org/I4210132349"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Kevin D. Murray","raw_affiliation_strings":["ARC Centre of Excellence in Plant Energy Biology; Australian National University"],"affiliations":[{"raw_affiliation_string":"ARC Centre of Excellence in Plant Energy Biology; Australian National University","institution_ids":["https://openalex.org/I4210102918","https://openalex.org/I118347636"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064104059","display_name":"Russell Y. Neches","orcid":"https://orcid.org/0000-0002-2055-8381"},"institutions":[{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Russell Neches","raw_affiliation_strings":["Microbiology Graduate Group; Univerity of California, Davis"],"affiliations":[{"raw_affiliation_string":"Microbiology Graduate Group; Univerity of California, Davis","institution_ids":["https://openalex.org/I84218800"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039305636","display_name":"Camille Scott","orcid":"https://orcid.org/0000-0001-8822-8779"},"institutions":[{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Camille Scott","raw_affiliation_strings":["Lab for Data Intensive Biology; School of Veterinary Medicine; University of California, Davis"],"affiliations":[{"raw_affiliation_string":"Lab for Data Intensive Biology; School of Veterinary Medicine; University of California, Davis","institution_ids":["https://openalex.org/I84218800"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102729737","display_name":"Ryan Shean","orcid":"https://orcid.org/0000-0002-2831-8040"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ryan Shean","raw_affiliation_strings":["University of Washington"],"affiliations":[{"raw_affiliation_string":"University of Washington","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048978715","display_name":"Sascha Steinbiss","orcid":null},"institutions":[{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sascha Steinbiss","raw_affiliation_strings":["Computer Science Graduate Group; University of California, Davis","Department of Population Health and Reproduction; School of Veterinary Medicine; University of California, Davis","Molecular, Cellular, and Integrative Physiology Graduate Group; University of California, Davis"],"affiliations":[{"raw_affiliation_string":"Computer Science Graduate Group; University of California, Davis","institution_ids":["https://openalex.org/I84218800"]},{"raw_affiliation_string":"Department of Population Health and Reproduction; School of Veterinary Medicine; University of California, Davis","institution_ids":["https://openalex.org/I84218800"]},{"raw_affiliation_string":"Molecular, Cellular, and Integrative Physiology Graduate Group; University of California, Davis","institution_ids":["https://openalex.org/I84218800"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089110395","display_name":"Cait Sydney","orcid":null},"institutions":[{"id":"https://openalex.org/I1291425158","display_name":"Google (United States)","ror":"https://ror.org/00njsd438","country_code":"US","type":"company","lineage":["https://openalex.org/I1291425158","https://openalex.org/I4210128969"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cait Sydney","raw_affiliation_strings":["Google, Inc"],"affiliations":[{"raw_affiliation_string":"Google, Inc","institution_ids":["https://openalex.org/I1291425158"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5036229691","display_name":"C. Titus Brown","orcid":"https://orcid.org/0000-0001-6001-2677"},"institutions":[{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"C. Titus Brown","raw_affiliation_strings":["Lab for Data Intensive Biology; School of Veterinary Medicine; University of California, Davis"],"affiliations":[{"raw_affiliation_string":"Lab for Data Intensive Biology; School of Veterinary Medicine; University of California, Davis","institution_ids":["https://openalex.org/I84218800"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":15,"corresponding_author_ids":["https://openalex.org/A5048840870"],"corresponding_institution_ids":["https://openalex.org/I84218800"],"apc_list":null,"apc_paid":null,"fwci":0.5597,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.6620489,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"2","issue":"15","first_page":"272","last_page":"272"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9857000112533569,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9857000112533569,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9739000201225281,"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/T11482","display_name":"RNA modifications and cancer","score":0.972100019454956,"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/sequence","display_name":"Sequence (biology)","score":0.5474425554275513},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4609445035457611},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.412864625453949},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4055395722389221},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3507246971130371},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.20368307828903198},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.09449499845504761}],"concepts":[{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5474425554275513},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4609445035457611},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.412864625453949},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4055395722389221},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3507246971130371},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.20368307828903198},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.09449499845504761}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.21105/joss.00272","is_oa":true,"landing_page_url":"https://doi.org/10.21105/joss.00272","pdf_url":"https://joss.theoj.org/papers/10.21105/joss.00272.pdf","source":{"id":"https://openalex.org/S4210214273","display_name":"The Journal of Open Source Software","issn_l":"2475-9066","issn":["2475-9066"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315853","host_organization_name":"Open Journals","host_organization_lineage":["https://openalex.org/P4310315853"],"host_organization_lineage_names":["Open Journals"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The Journal of Open Source Software","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.21105/joss.00272","is_oa":true,"landing_page_url":"https://doi.org/10.21105/joss.00272","pdf_url":"https://joss.theoj.org/papers/10.21105/joss.00272.pdf","source":{"id":"https://openalex.org/S4210214273","display_name":"The Journal of Open Source Software","issn_l":"2475-9066","issn":["2475-9066"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315853","host_organization_name":"Open Journals","host_organization_lineage":["https://openalex.org/P4310315853"],"host_organization_lineage_names":["Open Journals"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The Journal of Open Source Software","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.49000000953674316,"display_name":"Zero hunger","id":"https://metadata.un.org/sdg/2"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2725252423.pdf","grobid_xml":"https://content.openalex.org/works/W2725252423.grobid-xml"},"referenced_works_count":6,"referenced_works":["https://openalex.org/W282286282","https://openalex.org/W1912338927","https://openalex.org/W1954100204","https://openalex.org/W2115546424","https://openalex.org/W2163830511","https://openalex.org/W6602124240"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2082860237","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W1641042124","https://openalex.org/W2013243191","https://openalex.org/W2151865869","https://openalex.org/W2117258802"],"abstract_inverted_index":null,"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1}],"updated_date":"2026-03-27T14:29:43.386196","created_date":"2025-10-10T00:00:00"}
