{"id":"https://openalex.org/W4315928336","doi":"https://doi.org/10.1093/bioinformatics/btad028","title":"Mapache: a flexible pipeline to map ancient DNA","display_name":"Mapache: a flexible pipeline to map ancient DNA","publication_year":2023,"publication_date":"2023-01-13","ids":{"openalex":"https://openalex.org/W4315928336","doi":"https://doi.org/10.1093/bioinformatics/btad028","pmid":"https://pubmed.ncbi.nlm.nih.gov/36637197"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad028","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad028","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/2/btad028/49121126/btad028.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/article-pdf/39/2/btad028/49121126/btad028.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5003077340","display_name":"Samuel Neuenschwander","orcid":"https://orcid.org/0000-0002-4080-5546"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I97565354","display_name":"University of Lausanne","ror":"https://ror.org/019whta54","country_code":"CH","type":"education","lineage":["https://openalex.org/I97565354"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Samuel Neuenschwander","raw_affiliation_strings":["Department of Computational Biology, University of Lausanne , Lausanne 1015, Switzerland","Vital-IT, Swiss Institute of Bioinformatics , Lausanne 1015, Switzerland"],"raw_orcid":"https://orcid.org/0000-0002-4080-5546","affiliations":[{"raw_affiliation_string":"Department of Computational Biology, University of Lausanne , Lausanne 1015, Switzerland","institution_ids":["https://openalex.org/I97565354"]},{"raw_affiliation_string":"Vital-IT, Swiss Institute of Bioinformatics , Lausanne 1015, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029560002","display_name":"Diana Ivette Cruz D\u00e1valos","orcid":"https://orcid.org/0000-0002-5309-6937"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I97565354","display_name":"University of Lausanne","ror":"https://ror.org/019whta54","country_code":"CH","type":"education","lineage":["https://openalex.org/I97565354"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Diana I Cruz D\u00e1valos","raw_affiliation_strings":["Department of Computational Biology, University of Lausanne , Lausanne 1015, Switzerland","Swiss Institute of Bioinformatics , Lausanne 1015, Switzerland"],"raw_orcid":"https://orcid.org/0000-0002-5309-6937","affiliations":[{"raw_affiliation_string":"Department of Computational Biology, University of Lausanne , Lausanne 1015, Switzerland","institution_ids":["https://openalex.org/I97565354"]},{"raw_affiliation_string":"Swiss Institute of Bioinformatics , Lausanne 1015, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009500530","display_name":"Lucas Anchieri","orcid":"https://orcid.org/0000-0001-9828-7692"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I97565354","display_name":"University of Lausanne","ror":"https://ror.org/019whta54","country_code":"CH","type":"education","lineage":["https://openalex.org/I97565354"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Lucas Anchieri","raw_affiliation_strings":["Department of Computational Biology, University of Lausanne , Lausanne 1015, Switzerland","Swiss Institute of Bioinformatics , Lausanne 1015, Switzerland"],"raw_orcid":"https://orcid.org/0000-0001-9828-7692","affiliations":[{"raw_affiliation_string":"Department of Computational Biology, University of Lausanne , Lausanne 1015, Switzerland","institution_ids":["https://openalex.org/I97565354"]},{"raw_affiliation_string":"Swiss Institute of Bioinformatics , Lausanne 1015, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091411799","display_name":"B\u00e1rbara Sousa da Mota","orcid":"https://orcid.org/0000-0002-5062-6234"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I97565354","display_name":"University of Lausanne","ror":"https://ror.org/019whta54","country_code":"CH","type":"education","lineage":["https://openalex.org/I97565354"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"B\u00e1rbara Sousa da Mota","raw_affiliation_strings":["Department of Computational Biology, University of Lausanne , Lausanne 1015, Switzerland","Swiss Institute of Bioinformatics , Lausanne 1015, Switzerland"],"raw_orcid":"https://orcid.org/0000-0002-5062-6234","affiliations":[{"raw_affiliation_string":"Department of Computational Biology, University of Lausanne , Lausanne 1015, Switzerland","institution_ids":["https://openalex.org/I97565354"]},{"raw_affiliation_string":"Swiss Institute of Bioinformatics , Lausanne 1015, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064090398","display_name":"Davide Bozzi","orcid":"https://orcid.org/0000-0002-4828-356X"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I97565354","display_name":"University of Lausanne","ror":"https://ror.org/019whta54","country_code":"CH","type":"education","lineage":["https://openalex.org/I97565354"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Davide Bozzi","raw_affiliation_strings":["Department of Computational Biology, University of Lausanne , Lausanne 1015, Switzerland","Swiss Institute of Bioinformatics , Lausanne 1015, Switzerland"],"raw_orcid":"https://orcid.org/0000-0002-4828-356X","affiliations":[{"raw_affiliation_string":"Department of Computational Biology, University of Lausanne , Lausanne 1015, Switzerland","institution_ids":["https://openalex.org/I97565354"]},{"raw_affiliation_string":"Swiss Institute of Bioinformatics , Lausanne 1015, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030162729","display_name":"Simone Rubinacci","orcid":"https://orcid.org/0000-0002-7725-4813"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I97565354","display_name":"University of Lausanne","ror":"https://ror.org/019whta54","country_code":"CH","type":"education","lineage":["https://openalex.org/I97565354"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Simone Rubinacci","raw_affiliation_strings":["Department of Computational Biology, University of Lausanne , Lausanne 1015, Switzerland","Swiss Institute of Bioinformatics , Lausanne 1015, Switzerland"],"raw_orcid":"https://orcid.org/0000-0002-7725-4813","affiliations":[{"raw_affiliation_string":"Department of Computational Biology, University of Lausanne , Lausanne 1015, Switzerland","institution_ids":["https://openalex.org/I97565354"]},{"raw_affiliation_string":"Swiss Institute of Bioinformatics , Lausanne 1015, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031990107","display_name":"Olivier Delaneau","orcid":"https://orcid.org/0000-0002-3906-8446"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I97565354","display_name":"University of Lausanne","ror":"https://ror.org/019whta54","country_code":"CH","type":"education","lineage":["https://openalex.org/I97565354"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Olivier Delaneau","raw_affiliation_strings":["Department of Computational Biology, University of Lausanne , Lausanne 1015, Switzerland","Swiss Institute of Bioinformatics , Lausanne 1015, Switzerland"],"raw_orcid":"https://orcid.org/0000-0002-3906-8446","affiliations":[{"raw_affiliation_string":"Department of Computational Biology, University of Lausanne , Lausanne 1015, Switzerland","institution_ids":["https://openalex.org/I97565354"]},{"raw_affiliation_string":"Swiss Institute of Bioinformatics , Lausanne 1015, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072477553","display_name":"Simon Rasmussen","orcid":"https://orcid.org/0000-0001-6323-9041"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]},{"id":"https://openalex.org/I2801134892","display_name":"Novo Nordisk Foundation","ror":"https://ror.org/04txyc737","country_code":"DK","type":"facility","lineage":["https://openalex.org/I2801134892"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Simon Rasmussen","raw_affiliation_strings":["Novo Nordisk Foundation Center for Protein Research, University of Copenhagen , Copenhagen 2200, Denmark"],"raw_orcid":"https://orcid.org/0000-0001-6323-9041","affiliations":[{"raw_affiliation_string":"Novo Nordisk Foundation Center for Protein Research, University of Copenhagen , Copenhagen 2200, Denmark","institution_ids":["https://openalex.org/I2801134892","https://openalex.org/I124055696"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064314813","display_name":"Anna\u2010Sapfo Malaspinas","orcid":"https://orcid.org/0000-0003-1001-7511"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I97565354","display_name":"University of Lausanne","ror":"https://ror.org/019whta54","country_code":"CH","type":"education","lineage":["https://openalex.org/I97565354"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Anna-Sapfo Malaspinas","raw_affiliation_strings":["Department of Computational Biology, University of Lausanne , Lausanne 1015, Switzerland","Swiss Institute of Bioinformatics , Lausanne 1015, Switzerland"],"raw_orcid":"https://orcid.org/0000-0003-1001-7511","affiliations":[{"raw_affiliation_string":"Department of Computational Biology, University of Lausanne , Lausanne 1015, Switzerland","institution_ids":["https://openalex.org/I97565354"]},{"raw_affiliation_string":"Swiss Institute of Bioinformatics , Lausanne 1015, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5003077340"],"corresponding_institution_ids":["https://openalex.org/I12708293","https://openalex.org/I97565354"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":4088,"currency":"EUR","value_usd":4408},"fwci":5.3882,"has_fulltext":true,"cited_by_count":18,"citation_normalized_percentile":{"value":0.95849595,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"39","issue":"2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10751","display_name":"Forensic and Genetic Research","score":0.7723000049591064,"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"}},"topics":[{"id":"https://openalex.org/T10751","display_name":"Forensic and Genetic Research","score":0.7723000049591064,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.08460000157356262,"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/T12090","display_name":"Language and cultural evolution","score":0.01759999990463257,"subfield":{"id":"https://openalex.org/subfields/3316","display_name":"Cultural Studies"},"field":{"id":"https://openalex.org/fields/33","display_name":"Social Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.8038187026977539},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6113946437835693},{"id":"https://openalex.org/keywords/ancient-dna","display_name":"Ancient DNA","score":0.5412416458129883},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4499363899230957},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.4387814402580261},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.39164745807647705},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.23745590448379517},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2227500081062317},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.19827964901924133},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.05750519037246704}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.8038187026977539},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6113946437835693},{"id":"https://openalex.org/C189338579","wikidata":"https://www.wikidata.org/wiki/Q290447","display_name":"Ancient DNA","level":3,"score":0.5412416458129883},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4499363899230957},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.4387814402580261},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.39164745807647705},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.23745590448379517},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2227500081062317},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.19827964901924133},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.05750519037246704},{"id":"https://openalex.org/C99454951","wikidata":"https://www.wikidata.org/wiki/Q932068","display_name":"Environmental health","level":1,"score":0.0},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000072441","descriptor_name":"DNA, Ancient","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000072441","descriptor_name":"DNA, Ancient","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000072441","descriptor_name":"DNA, Ancient","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":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btad028","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad028","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/2/btad028/49121126/btad028.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:36637197","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36637197","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:9901408","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9901408","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC9901408/pdf/btad028.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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"},{"id":"pmh:oai:iris.unil.ch:iris/147910","is_oa":false,"landing_page_url":"https://iris.unil.ch/handle/iris/147910","pdf_url":null,"source":{"id":"https://openalex.org/S7407055444","display_name":"IRIS","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"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":"journal article"},{"id":"pmh:oai:pure.atira.dk:openaire_cris_publications/cc050f2f-ebf2-4452-8879-3db07f40c397","is_oa":true,"landing_page_url":"https://researchprofiles.ku.dk/da/publications/cc050f2f-ebf2-4452-8879-3db07f40c397","pdf_url":null,"source":{"id":"https://openalex.org/S4306401983","display_name":"Research at the University of Copenhagen (University of Copenhagen)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I124055696","host_organization_name":"University of Copenhagen","host_organization_lineage":["https://openalex.org/I124055696"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Neuenschwander , S , Cruz D\u00e1valos , D I , Anchieri , L , Sousa da Mota , B , Bozzi , D , Rubinacci , S , Delaneau , O , Rasmussen , S & Malaspinas , A-S 2023 , ' Mapache : a flexible pipeline to map ancient DNA ' , Bioinformatics (Online) , vol. 39 , no. 2 . https://doi.org/10.1093/bioinformatics/btad028","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad028","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad028","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/2/btad028/49121126/btad028.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/G2922463636","display_name":null,"funder_award_id":"PCEGP3_181251","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"}],"funders":[{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"},{"id":"https://openalex.org/F4320322436","display_name":"Novo Nordisk","ror":"https://ror.org/0435rc536"},{"id":"https://openalex.org/F4320325957","display_name":"Novo Nordisk Fonden","ror":"https://ror.org/04txyc737"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4315928336.pdf"},"referenced_works_count":21,"referenced_works":["https://openalex.org/W2070720545","https://openalex.org/W2102619694","https://openalex.org/W2103441770","https://openalex.org/W2111281047","https://openalex.org/W2126798272","https://openalex.org/W2150163641","https://openalex.org/W2168133698","https://openalex.org/W2170551349","https://openalex.org/W2263582186","https://openalex.org/W2319185332","https://openalex.org/W2432815617","https://openalex.org/W2951912016","https://openalex.org/W2953133001","https://openalex.org/W3120295425","https://openalex.org/W3122109253","https://openalex.org/W3131055609","https://openalex.org/W3136141030","https://openalex.org/W3158812111","https://openalex.org/W4210644165","https://openalex.org/W4286002085","https://openalex.org/W6675401170"],"related_works":["https://openalex.org/W2055197888","https://openalex.org/W2056560357","https://openalex.org/W1965491053","https://openalex.org/W2000099891","https://openalex.org/W2052673034","https://openalex.org/W2057597395","https://openalex.org/W2022778960","https://openalex.org/W2389619865","https://openalex.org/W2411524895","https://openalex.org/W2169403284"],"abstract_inverted_index":{"SUMMARY:":[0],"We":[1],"introduce":[2],"mapache,":[3],"a":[4,20],"flexible,":[5],"robust":[6],"and":[7,13,16,31,46,49],"scalable":[8],"pipeline":[9],"to":[10,38,54],"map,":[11],"quantify":[12],"impute":[14],"ancient":[15],"present-day":[17],"DNA":[18],"in":[19,26],"reproducible":[21],"way.":[22],"Mapache":[23,59,73],"is":[24,32,74,83],"implemented":[25],"the":[27],"workflow":[28],"manager":[29],"Snakemake":[30,68],"optimized":[33],"for":[34],"low-space":[35],"consumption,":[36],"allowing":[37],"efficiently":[39],"(re)map":[40],"large":[41],"datasets-such":[42],"as":[43],"reference":[44],"panels":[45],"multiple":[47],"extracts":[48],"libraries":[50],"per":[51],"sample":[52],"-":[53],"one":[55],"or":[56,64],"several":[57],"genomes.":[58],"can":[60],"easily":[61],"be":[62],"customized":[63],"combined":[65],"with":[66],"other":[67],"tools.":[69],"AVAILABILITY":[70],"AND":[71],"IMPLEMENTATION:":[72],"freely":[75],"available":[76,92],"on":[77],"GitHub":[78],"(https://github.com/sneuensc/mapache).":[79],"An":[80],"extensive":[81],"manual":[82],"provided":[84],"at":[85,93],"https://github.com/sneuensc/mapache/wiki.":[86],"SUPPLEMENTARY":[87],"INFORMATION:":[88],"Supplementary":[89],"data":[90],"are":[91],"Bioinformatics":[94],"online.":[95]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":6}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}