{"id":"https://openalex.org/W2999693165","doi":"https://doi.org/10.1093/bioinformatics/btz933","title":"HaploTypo: a variant-calling pipeline for phased genomes","display_name":"HaploTypo: a variant-calling pipeline for phased genomes","publication_year":2019,"publication_date":"2019-12-10","ids":{"openalex":"https://openalex.org/W2999693165","doi":"https://doi.org/10.1093/bioinformatics/btz933","mag":"2999693165","pmid":"https://pubmed.ncbi.nlm.nih.gov/31834373"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz933","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz933","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/8/2569/33116442/btz933.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/36/8/2569/33116442/btz933.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5045563136","display_name":"Cinta Pegueroles","orcid":"https://orcid.org/0000-0003-0701-9866"},"institutions":[{"id":"https://openalex.org/I4210137962","display_name":"Centre for Genomic Regulation","ror":"https://ror.org/03wyzt892","country_code":"ES","type":"funder","lineage":["https://openalex.org/I4210132884","https://openalex.org/I4210137962","https://openalex.org/I4387153040"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Cinta Pegueroles","raw_affiliation_strings":["Centre for Genomic Regulation, The Barcelona Institute of Science and Technology , Barcelona 08003, Spain"],"affiliations":[{"raw_affiliation_string":"Centre for Genomic Regulation, The Barcelona Institute of Science and Technology , Barcelona 08003, Spain","institution_ids":["https://openalex.org/I4210137962"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060927206","display_name":"Ver\u00f3nica Mix\u00e3o","orcid":"https://orcid.org/0000-0001-6669-0161"},"institutions":[{"id":"https://openalex.org/I4210137962","display_name":"Centre for Genomic Regulation","ror":"https://ror.org/03wyzt892","country_code":"ES","type":"funder","lineage":["https://openalex.org/I4210132884","https://openalex.org/I4210137962","https://openalex.org/I4387153040"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Ver\u00f3nica Mix\u00e3o","raw_affiliation_strings":["Centre for Genomic Regulation, The Barcelona Institute of Science and Technology , Barcelona 08003, Spain"],"affiliations":[{"raw_affiliation_string":"Centre for Genomic Regulation, The Barcelona Institute of Science and Technology , Barcelona 08003, Spain","institution_ids":["https://openalex.org/I4210137962"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026608239","display_name":"Laia Carret\u00e9","orcid":"https://orcid.org/0000-0002-0035-0356"},"institutions":[{"id":"https://openalex.org/I4210137962","display_name":"Centre for Genomic Regulation","ror":"https://ror.org/03wyzt892","country_code":"ES","type":"funder","lineage":["https://openalex.org/I4210132884","https://openalex.org/I4210137962","https://openalex.org/I4387153040"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Laia Carret\u00e9","raw_affiliation_strings":["Centre for Genomic Regulation, The Barcelona Institute of Science and Technology , Barcelona 08003, Spain"],"affiliations":[{"raw_affiliation_string":"Centre for Genomic Regulation, The Barcelona Institute of Science and Technology , Barcelona 08003, Spain","institution_ids":["https://openalex.org/I4210137962"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076347047","display_name":"Manu Molina","orcid":null},"institutions":[{"id":"https://openalex.org/I4210137962","display_name":"Centre for Genomic Regulation","ror":"https://ror.org/03wyzt892","country_code":"ES","type":"funder","lineage":["https://openalex.org/I4210132884","https://openalex.org/I4210137962","https://openalex.org/I4387153040"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Manu Molina","raw_affiliation_strings":["Centre for Genomic Regulation, The Barcelona Institute of Science and Technology , Barcelona 08003, Spain"],"affiliations":[{"raw_affiliation_string":"Centre for Genomic Regulation, The Barcelona Institute of Science and Technology , Barcelona 08003, Spain","institution_ids":["https://openalex.org/I4210137962"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003394700","display_name":"Toni Gabald\u00f3n","orcid":"https://orcid.org/0000-0003-0019-1735"},"institutions":[{"id":"https://openalex.org/I11932220","display_name":"Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats","ror":"https://ror.org/0371hy230","country_code":"ES","type":"nonprofit","lineage":["https://openalex.org/I11932220"]},{"id":"https://openalex.org/I170486558","display_name":"Pompeu Fabra University","ror":"https://ror.org/04n0g0b29","country_code":"ES","type":"education","lineage":["https://openalex.org/I170486558"]},{"id":"https://openalex.org/I4210137962","display_name":"Centre for Genomic Regulation","ror":"https://ror.org/03wyzt892","country_code":"ES","type":"funder","lineage":["https://openalex.org/I4210132884","https://openalex.org/I4210137962","https://openalex.org/I4387153040"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Toni Gabald\u00f3n","raw_affiliation_strings":["Centre for Genomic Regulation, The Barcelona Institute of Science and Technology , Barcelona 08003, Spain","ICREA , Barcelona 08010, Spain","Universitat Pompeu Fabra (UPF) , Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"Centre for Genomic Regulation, The Barcelona Institute of Science and Technology , Barcelona 08003, Spain","institution_ids":["https://openalex.org/I4210137962"]},{"raw_affiliation_string":"ICREA , Barcelona 08010, Spain","institution_ids":["https://openalex.org/I11932220"]},{"raw_affiliation_string":"Universitat Pompeu Fabra (UPF) , Barcelona, Spain","institution_ids":["https://openalex.org/I170486558"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5003394700","https://openalex.org/A5045563136","https://openalex.org/A5060927206","https://openalex.org/A5076347047"],"corresponding_institution_ids":["https://openalex.org/I11932220","https://openalex.org/I170486558","https://openalex.org/I4210137962"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.7751,"has_fulltext":false,"cited_by_count":32,"citation_normalized_percentile":{"value":0.71923912,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"36","issue":"8","first_page":"2569","last_page":"2571"},"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/T10012","display_name":"Genetic diversity and population structure","score":0.9976999759674072,"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"}},{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9955000281333923,"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/pipeline","display_name":"Pipeline (software)","score":0.8593652844429016},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6135348081588745},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5773832201957703},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4565134048461914},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3198360800743103},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.31153345108032227},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2572888135910034},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11332333087921143}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.8593652844429016},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6135348081588745},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5773832201957703},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4565134048461914},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3198360800743103},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.31153345108032227},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2572888135910034},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11332333087921143}],"mesh":[{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006579","descriptor_name":"Heterozygote","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006579","descriptor_name":"Heterozygote","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006579","descriptor_name":"Heterozygote","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":"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}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btz933","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz933","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/8/2569/33116442/btz933.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31834373","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31834373","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:repositori-api.upf.edu:10230/44539","is_oa":true,"landing_page_url":"http://hdl.handle.net/10230/44539","pdf_url":null,"source":{"id":"https://openalex.org/S4306402615","display_name":"Repositori digital de la UPF (Universitat Pompeu Fabra)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I170486558","host_organization_name":"Universitat Pompeu Fabra","host_organization_lineage":["https://openalex.org/I170486558"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:ddd.uab.cat:325129","is_oa":false,"landing_page_url":"https://ddd.uab.cat/record/325129","pdf_url":null,"source":{"id":"https://openalex.org/S4306400380","display_name":"Dip\u00f2sit Digital de Documents de la UAB (Universitat Aut\u00f2noma de Barcelona)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I123044942","host_organization_name":"Universitat Aut\u00f2noma de Barcelona","host_organization_lineage":["https://openalex.org/I123044942"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7178392","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7178392","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":"doi:10.1093/bioinformatics/btz933","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz933","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/8/2569/33116442/btz933.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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/F4320335322","display_name":"European Regional Development Fund","ror":"https://ror.org/00k4n6c32"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2999693165.pdf","grobid_xml":"https://content.openalex.org/works/W2999693165.grobid-xml"},"referenced_works_count":14,"referenced_works":["https://openalex.org/W1923694921","https://openalex.org/W1970326092","https://openalex.org/W2038511295","https://openalex.org/W2044182048","https://openalex.org/W2119180969","https://openalex.org/W2145518850","https://openalex.org/W2150131459","https://openalex.org/W2344852138","https://openalex.org/W2538143681","https://openalex.org/W2558089559","https://openalex.org/W2560383108","https://openalex.org/W2731392871","https://openalex.org/W2805097482","https://openalex.org/W2950587246"],"related_works":["https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W1971568933","https://openalex.org/W2013243191","https://openalex.org/W2117258802"],"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":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":21},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":4}],"updated_date":"2026-03-05T09:29:38.588285","created_date":"2020-01-23T00:00:00"}