{"id":"https://openalex.org/W4412088082","doi":"https://doi.org/10.1093/bioinformatics/btaf388","title":"Agptools: a utility suite for editing genome assemblies","display_name":"Agptools: a utility suite for editing genome assemblies","publication_year":2025,"publication_date":"2025-07-01","ids":{"openalex":"https://openalex.org/W4412088082","doi":"https://doi.org/10.1093/bioinformatics/btaf388","pmid":"https://pubmed.ncbi.nlm.nih.gov/40622245"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf388","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf388","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf388/63688159/btaf388.pdf","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://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf388/63688159/btaf388.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5106413248","display_name":"Edward S. Ricemeyer","orcid":null},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]},{"id":"https://openalex.org/I8204097","display_name":"Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen","ror":"https://ror.org/05591te55","country_code":"DE","type":"education","lineage":["https://openalex.org/I8204097"]}],"countries":["DE","US"],"is_corresponding":true,"raw_author_name":"Edward S Ricemeyer","raw_affiliation_strings":["Bond Life Sciences Center, University of Missouri , Columbia, MO 65221,","Palaeogenomics Group, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen , Munich 80539,","Bond Life Sciences Center, University of Missouri, Columbia, MO 65221, United States"],"affiliations":[{"raw_affiliation_string":"Bond Life Sciences Center, University of Missouri , Columbia, MO 65221,","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Palaeogenomics Group, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen , Munich 80539,","institution_ids":["https://openalex.org/I8204097"]},{"raw_affiliation_string":"Bond Life Sciences Center, University of Missouri, Columbia, MO 65221, United States","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033053548","display_name":"Rachel A Carroll","orcid":"https://orcid.org/0000-0002-4332-7148"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rachel A Carroll","raw_affiliation_strings":["Bond Life Sciences Center, University of Missouri , Columbia, MO 65221,","Bond Life Sciences Center, University of Missouri, Columbia, MO 65221, United States"],"affiliations":[{"raw_affiliation_string":"Bond Life Sciences Center, University of Missouri , Columbia, MO 65221,","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Bond Life Sciences Center, University of Missouri, Columbia, MO 65221, United States","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5062335998","display_name":"Wesley C. Warren","orcid":"https://orcid.org/0000-0003-2255-2730"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wesley C Warren","raw_affiliation_strings":["Bond Life Sciences Center, University of Missouri , Columbia, MO 65221,","Division of Animal Sciences, Department of Surgery, University of Missouri , Columbia, MO 65201,","Division of Animal Sciences, Department of Surgery, University of Missouri, Columbia, MO 65201, United States"],"affiliations":[{"raw_affiliation_string":"Bond Life Sciences Center, University of Missouri , Columbia, MO 65221,","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Division of Animal Sciences, Department of Surgery, University of Missouri , Columbia, MO 65201,","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Division of Animal Sciences, Department of Surgery, University of Missouri, Columbia, MO 65201, United States","institution_ids":["https://openalex.org/I76835614"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5106413248"],"corresponding_institution_ids":["https://openalex.org/I76835614","https://openalex.org/I8204097"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.8073,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.73936473,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"41","issue":"7","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9979000091552734,"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/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9979000091552734,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9879000186920166,"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/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9722999930381775,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/suite","display_name":"Suite","score":0.8305450081825256},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6712749004364014},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4217844009399414},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3972143530845642},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.38032081723213196},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.23566192388534546},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1812831461429596},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08938759565353394},{"id":"https://openalex.org/keywords/geography","display_name":"Geography","score":0.06278404593467712}],"concepts":[{"id":"https://openalex.org/C79581498","wikidata":"https://www.wikidata.org/wiki/Q1367530","display_name":"Suite","level":2,"score":0.8305450081825256},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6712749004364014},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4217844009399414},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3972143530845642},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.38032081723213196},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23566192388534546},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1812831461429596},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08938759565353394},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.06278404593467712},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","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":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","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":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf388","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf388","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf388/63688159/btaf388.pdf","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:40622245","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40622245","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:12286700","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12286700","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/btaf388","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf388","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf388/63688159/btaf388.pdf","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":[{"id":"https://openalex.org/G8810317129","display_name":null,"funder_award_id":"NSF DBI 1940624","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4412088082.pdf","grobid_xml":"https://content.openalex.org/works/W4412088082.grobid-xml"},"referenced_works_count":22,"referenced_works":["https://openalex.org/W2241763745","https://openalex.org/W2607669908","https://openalex.org/W2903541438","https://openalex.org/W2969330652","https://openalex.org/W3146275690","https://openalex.org/W3159728495","https://openalex.org/W3178540789","https://openalex.org/W3198374781","https://openalex.org/W4220668127","https://openalex.org/W4220999759","https://openalex.org/W4223416923","https://openalex.org/W4311663808","https://openalex.org/W4311928790","https://openalex.org/W4321112378","https://openalex.org/W4377289885","https://openalex.org/W4381251865","https://openalex.org/W4391104625","https://openalex.org/W4393969973","https://openalex.org/W4396803203","https://openalex.org/W4398183057","https://openalex.org/W4402907669","https://openalex.org/W6690241230"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W4231704780","https://openalex.org/W2083794993","https://openalex.org/W352609212","https://openalex.org/W4404692318","https://openalex.org/W4200340037","https://openalex.org/W1511772879","https://openalex.org/W4379115841"],"abstract_inverted_index":{"Source":[0],"code":[1],"and":[2,13],"binaries":[3],"freely":[4],"available":[5],"for":[6],"download":[7],"at":[8],"https://github.com/WarrenLab/agptools,":[9],"implemented":[10],"in":[11],"Python":[12],"supported":[14],"on":[15],"all":[16],"operating":[17],"systems.":[18]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
