{"id":"https://openalex.org/W2999357634","doi":"https://doi.org/10.1093/bioinformatics/btz966","title":"ipyrad: Interactive assembly and analysis of RADseq datasets","display_name":"ipyrad: Interactive assembly and analysis of RADseq datasets","publication_year":2019,"publication_date":"2019-12-31","ids":{"openalex":"https://openalex.org/W2999357634","doi":"https://doi.org/10.1093/bioinformatics/btz966","mag":"2999357634","pmid":"https://pubmed.ncbi.nlm.nih.gov/31904816"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz966","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz966","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/8/2592/33116612/btz966.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":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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/36/8/2592/33116612/btz966.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5079421225","display_name":"Deren A. R. Eaton","orcid":"https://orcid.org/0000-0002-5922-2770"},"institutions":[{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Deren A R Eaton","raw_affiliation_strings":["Department of Ecology, Evolution, and Environmental Biology , Columbia University, New York, NY 10027, USA"],"affiliations":[{"raw_affiliation_string":"Department of Ecology, Evolution, and Environmental Biology , Columbia University, New York, NY 10027, USA","institution_ids":["https://openalex.org/I78577930"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080090882","display_name":"Isaac Overcast","orcid":"https://orcid.org/0000-0001-8614-6892"},"institutions":[{"id":"https://openalex.org/I174216632","display_name":"City University of New York","ror":"https://ror.org/00453a208","country_code":"US","type":"education","lineage":["https://openalex.org/I174216632"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Isaac Overcast","raw_affiliation_strings":["Department of Biology, Graduate School, University Center of the City University of New York , New York, NY 10016, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biology, Graduate School, University Center of the City University of New York , New York, NY 10016, USA","institution_ids":["https://openalex.org/I174216632"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5079421225"],"corresponding_institution_ids":["https://openalex.org/I78577930"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":30.2344,"has_fulltext":false,"cited_by_count":877,"citation_normalized_percentile":{"value":0.99839443,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"36","issue":"8","first_page":"2592","last_page":"2594"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9990000128746033,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9977999925613403,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.9097225069999695},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8499845266342163},{"id":"https://openalex.org/keywords/scripting-language","display_name":"Scripting language","score":0.8049456477165222},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.6982408165931702},{"id":"https://openalex.org/keywords/suite","display_name":"Suite","score":0.6860531568527222},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.6718097925186157},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.6594073176383972},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.6475775241851807},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.5142076015472412},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.4978978633880615},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4579658806324005},{"id":"https://openalex.org/keywords/codebase","display_name":"Codebase","score":0.4458059072494507},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.41828659176826477},{"id":"https://openalex.org/keywords/rapid-prototyping","display_name":"Rapid prototyping","score":0.4149426221847534},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.3781800866127014},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.36264050006866455}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.9097225069999695},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8499845266342163},{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.8049456477165222},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.6982408165931702},{"id":"https://openalex.org/C79581498","wikidata":"https://www.wikidata.org/wiki/Q1367530","display_name":"Suite","level":2,"score":0.6860531568527222},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.6718097925186157},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.6594073176383972},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.6475775241851807},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.5142076015472412},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.4978978633880615},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4579658806324005},{"id":"https://openalex.org/C51929080","wikidata":"https://www.wikidata.org/wiki/Q2425187","display_name":"Codebase","level":3,"score":0.4458059072494507},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.41828659176826477},{"id":"https://openalex.org/C2780395129","wikidata":"https://www.wikidata.org/wiki/Q1128971","display_name":"Rapid prototyping","level":2,"score":0.4149426221847534},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.3781800866127014},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.36264050006866455},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"score":0.0},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","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/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004282","descriptor_name":"Documentation","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}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btz966","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz966","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/8/2592/33116612/btz966.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31904816","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31904816","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btz966","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz966","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/8/2592/33116612/btz966.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G140466501","display_name":null,"funder_award_id":"DEB 1745562","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G1517414975","display_name":null,"funder_award_id":"DEB-1557059","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4787082615","display_name":null,"funder_award_id":"DEB-1253710","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7404482930","display_name":null,"funder_award_id":"BIOTA, 2013/50297-0","funder_id":"https://openalex.org/F4320320997","funder_display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320320997","display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo","ror":"https://ror.org/02ddkpn78"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2999357634.pdf","grobid_xml":"https://content.openalex.org/works/W2999357634.grobid-xml"},"referenced_works_count":39,"referenced_works":["https://openalex.org/W2005228725","https://openalex.org/W2036897871","https://openalex.org/W2039486775","https://openalex.org/W2081612620","https://openalex.org/W2085315239","https://openalex.org/W2093044565","https://openalex.org/W2095882149","https://openalex.org/W2098126593","https://openalex.org/W2103441770","https://openalex.org/W2104450455","https://openalex.org/W2108234281","https://openalex.org/W2108524369","https://openalex.org/W2108675949","https://openalex.org/W2125855697","https://openalex.org/W2127305711","https://openalex.org/W2132926880","https://openalex.org/W2136430672","https://openalex.org/W2141052558","https://openalex.org/W2146346510","https://openalex.org/W2159474015","https://openalex.org/W2161184021","https://openalex.org/W2169773990","https://openalex.org/W2170676344","https://openalex.org/W2263977295","https://openalex.org/W2344301702","https://openalex.org/W2470818520","https://openalex.org/W2513506562","https://openalex.org/W2518463443","https://openalex.org/W2553804235","https://openalex.org/W2600760682","https://openalex.org/W2795697644","https://openalex.org/W2913623770","https://openalex.org/W2951448261","https://openalex.org/W2971378941","https://openalex.org/W2976876706","https://openalex.org/W2979995063","https://openalex.org/W2980958588","https://openalex.org/W2982135793","https://openalex.org/W6768864122"],"related_works":["https://openalex.org/W2344367508","https://openalex.org/W2571988079","https://openalex.org/W2113128227","https://openalex.org/W632256878","https://openalex.org/W2491403535","https://openalex.org/W2479811461","https://openalex.org/W2098629748","https://openalex.org/W2104915799","https://openalex.org/W4311938462","https://openalex.org/W2144528247"],"abstract_inverted_index":{"ipyrad":[0],"is":[1,13],"a":[2],"free":[3],"and":[4,20,22,37,43],"open":[5],"source":[6],"program":[7],"written":[8],"in":[9],"Python.":[10],"Source":[11],"code":[12],"available":[14,50],"from":[15],"the":[16,28],"GitHub":[17],"repository":[18],"(https://github.com/dereneaton/ipyrad/),":[19],"Linux":[21],"MacOS":[23],"installs":[24],"are":[25,49],"distributed":[26],"through":[27],"conda":[29],"package":[30],"manager.":[31],"Complete":[32],"documentation,":[33],"including":[34],"numerous":[35],"tutorials,":[36],"Jupyter":[38],"notebooks":[39],"demonstrating":[40],"example":[41],"assemblies":[42],"applications":[44],"of":[45],"downstream":[46],"analysis":[47],"tools":[48],"online:":[51],"https://ipyrad.readthedocs.io/.":[52]},"counts_by_year":[{"year":2026,"cited_by_count":41},{"year":2025,"cited_by_count":154},{"year":2024,"cited_by_count":159},{"year":2023,"cited_by_count":166},{"year":2022,"cited_by_count":151},{"year":2021,"cited_by_count":126},{"year":2020,"cited_by_count":60},{"year":2019,"cited_by_count":15},{"year":2018,"cited_by_count":4}],"updated_date":"2026-04-20T07:46:08.049788","created_date":"2025-10-10T00:00:00"}
