{"id":"https://openalex.org/W3026538346","doi":"https://doi.org/10.1186/s12859-020-3475-0","title":"PACVr: plastome assembly coverage visualization in R","display_name":"PACVr: plastome assembly coverage visualization in R","publication_year":2020,"publication_date":"2020-05-24","ids":{"openalex":"https://openalex.org/W3026538346","doi":"https://doi.org/10.1186/s12859-020-3475-0","mag":"3026538346","pmid":"https://pubmed.ncbi.nlm.nih.gov/32448146","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/7245912"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-020-3475-0","doi":"https://doi.org/10.1186/s12859-020-3475-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-3475-0","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-3475-0","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","ccf-c","cwts-core","doaj","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-2","oarl","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-3475-0","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5021224578","display_name":"Michael Gruenstaeudl","orcid":"https://orcid.org/0000-0002-1666-1773","observed_orcids":["https://orcid.org/0000-0002-1666-1773"]},"institutions":[{"id":"https://openalex.org/I75951250","display_name":"Freie Universit\u00e4t Berlin","ror":"https://ror.org/046ak2485","country_code":"DE","type":"education","lineage":["https://openalex.org/I75951250"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Michael Gruenstaeudl","raw_affiliation_strings":["Institut f\u00fcr Biologie, Freie Universit\u00e4t Berlin, 14195 Berlin, Germany","Institut f\u00fcr Biologie, Systematische Botanik und Pflanzengeographie, Freie Universit\u00e4t Berlin, Berlin, 14195, Germany"],"raw_orcid":"https://orcid.org/0000-0002-1666-1773","affiliations":[{"raw_affiliation_string":"Institut f\u00fcr Biologie, Freie Universit\u00e4t Berlin, 14195 Berlin, Germany","institution_ids":["https://openalex.org/I75951250"]},{"raw_affiliation_string":"Institut f\u00fcr Biologie, Systematische Botanik und Pflanzengeographie, Freie Universit\u00e4t Berlin, Berlin, 14195, Germany","institution_ids":["https://openalex.org/I75951250"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006492347","display_name":"Nils Jenke","orcid":"https://orcid.org/0009-0006-2481-6196","observed_orcids":["https://orcid.org/0009-0006-2481-6196"]},"institutions":[{"id":"https://openalex.org/I75951250","display_name":"Freie Universit\u00e4t Berlin","ror":"https://ror.org/046ak2485","country_code":"DE","type":"education","lineage":["https://openalex.org/I75951250"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Nils Jenke","raw_affiliation_strings":["Institut f\u00fcr Bioinformatik, Freie Universit\u00e4t Berlin, 14195 Berlin, Germany","Institut f\u00fcr Bioinformatik, Freie Universit\u00e4t Berlin, Berlin, 14195, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut f\u00fcr Bioinformatik, Freie Universit\u00e4t Berlin, 14195 Berlin, Germany","institution_ids":["https://openalex.org/I75951250"]},{"raw_affiliation_string":"Institut f\u00fcr Bioinformatik, Freie Universit\u00e4t Berlin, Berlin, 14195, Germany","institution_ids":["https://openalex.org/I75951250"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5021224578"],"corresponding_institution_ids":["https://openalex.org/I75951250"],"apc_list":{"value":2170,"currency":"USD","value_usd":2170},"apc_paid":{"value":2170,"currency":"USD","value_usd":2170},"fwci":14.1792,"has_fulltext":true,"cited_by_count":342,"citation_normalized_percentile":{"value":0.99591283,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"21","issue":"1","first_page":"207","last_page":"207"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9951000213623047,"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":0.9951000213623047,"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/T10385","display_name":"Plant Diversity and Evolution","score":0.00139999995008111,"subfield":{"id":"https://openalex.org/subfields/1105","display_name":"Ecology, Evolution, Behavior and Systematics"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.0013000000035390258,"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/chloroplast-genome","display_name":"chloroplast genome","score":0.800000011920929},{"id":"https://openalex.org/keywords/quadripartite-genome-structure","display_name":"quadripartite genome structure","score":0.8679999709129333},{"id":"https://openalex.org/keywords/inverted-repeats","display_name":"inverted repeats","score":0.9160000085830688},{"id":"https://openalex.org/keywords/synteny","display_name":"synteny","score":0.972000002861023},{"id":"https://openalex.org/keywords/assembly-quality-control","display_name":"assembly quality control","score":0.9229999780654907},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.718999981880188}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.8493769764900208},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.7253395915031433},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.7011033296585083},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5412416458129883},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5393415093421936},{"id":"https://openalex.org/C93829228","wikidata":"https://www.wikidata.org/wiki/Q165963","display_name":"Plastid","level":4,"score":0.5368978977203369},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4285673499107361},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.42437633872032166},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3310580849647522},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.28561708331108093},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.16377076506614685},{"id":"https://openalex.org/C69305403","wikidata":"https://www.wikidata.org/wiki/Q47263","display_name":"Chloroplast","level":3,"score":0.09175169467926025},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.08548301458358765},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012091","descriptor_name":"Repetitive Sequences, Nucleic Acid","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054627","descriptor_name":"Genome, Plastid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":11,"locations":[{"id":"doi:10.1186/s12859-020-3475-0","doi":"https://doi.org/10.1186/s12859-020-3475-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-3475-0","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-3475-0","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","ccf-c","cwts-core","doaj","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-2","oarl","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"doi:10.1101/697821","doi":"https://doi.org/10.1101/697821","is_oa":true,"landing_page_url":"https://doi.org/10.1101/697821","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2019/07/11/697821.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmh:oai:pubmedcentral.nih.gov:7245912","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7245912","pdf_url":null,"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,"listed_in":[],"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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmid:32448146","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32448146","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,"listed_in":[],"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":"BMC bioinformatics","raw_type":"Journal Article"},{"id":"pmh:oai:scholars.fhsu.edu:biology_facpubs-1035","doi":null,"is_oa":true,"landing_page_url":"https://scholars.fhsu.edu/biology_facpubs/36","pdf_url":null,"source":{"id":"https://openalex.org/S4377196602","display_name":"FHSU Scholars Repository (Fort Hays State University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I91083438","host_organization_name":"Fort Hays State University","host_organization_lineage":["https://openalex.org/I91083438"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Biological Sciences Faculty Publications","raw_type":"text"},{"id":"pmh:oai:doaj.org/article:32994005de014452964bf16fb0cf9e88","doi":null,"is_oa":true,"landing_page_url":"https://doaj.org/article/32994005de014452964bf16fb0cf9e88","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 21, Iss 1, Pp 1-21 (2020)","raw_type":"article"},{"id":"pmh:oai:zenodo.org:3281834","doi":null,"is_oa":true,"landing_page_url":"https://zenodo.org/record/3281834","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"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":"","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:zenodo.org:3673838","doi":null,"is_oa":true,"landing_page_url":"https://zenodo.org/record/3673838","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"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":"","raw_type":"info:eu-repo/semantics/article"},{"id":"doi:10.5281/zenodo.3281833","doi":"https://doi.org/10.5281/zenodo.3281833","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.3281833","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article-journal"},{"id":"doi:10.5281/zenodo.3281834","doi":"https://doi.org/10.5281/zenodo.3281834","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.3281834","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article-journal"},{"id":"doi:10.5281/zenodo.3673838","doi":"https://doi.org/10.5281/zenodo.3673838","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.3673838","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.1186/s12859-020-3475-0","doi":"https://doi.org/10.1186/s12859-020-3475-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-3475-0","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-3475-0","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","ccf-c","cwts-core","doaj","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-2","oarl","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G3027536161","display_name":"PlastidenPhylogenomik von Seerosen, mit Schwerpunkt auf Partitionierungsstrategien und der Entwicklung bioinformatischer Methoden","funder_award_id":"418670221","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320324521","display_name":"Freie Universit\u00e4t Berlin","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3026538346.pdf","grobid_xml":"https://content.openalex.org/works/W3026538346.grobid-xml"},"referenced_works_count":109,"referenced_works":["https://openalex.org/W1622429627","https://openalex.org/W1878526919","https://openalex.org/W1899220380","https://openalex.org/W1916919897","https://openalex.org/W1921732794","https://openalex.org/W1924760575","https://openalex.org/W1935720352","https://openalex.org/W1966958281","https://openalex.org/W1973094248","https://openalex.org/W1973530293","https://openalex.org/W1978732934","https://openalex.org/W1995054497","https://openalex.org/W1996925108","https://openalex.org/W2028257373","https://openalex.org/W2051819126","https://openalex.org/W2060217102","https://openalex.org/W2060501712","https://openalex.org/W2065227864","https://openalex.org/W2065812850","https://openalex.org/W2065817684","https://openalex.org/W2071221957","https://openalex.org/W2076359272","https://openalex.org/W2077232789","https://openalex.org/W2077456155","https://openalex.org/W2078420731","https://openalex.org/W2087360477","https://openalex.org/W2096128575","https://openalex.org/W2099388167","https://openalex.org/W2102281081","https://openalex.org/W2103441770","https://openalex.org/W2105067980","https://openalex.org/W2105071916","https://openalex.org/W2107772251","https://openalex.org/W2108234281","https://openalex.org/W2110014529","https://openalex.org/W2118334191","https://openalex.org/W2120902911","https://openalex.org/W2124985265","https://openalex.org/W2128880918","https://openalex.org/W2129933858","https://openalex.org/W2134163401","https://openalex.org/W2135361281","https://openalex.org/W2136846721","https://openalex.org/W2139229065","https://openalex.org/W2141637710","https://openalex.org/W2141920662","https://openalex.org/W2142845224","https://openalex.org/W2151309250","https://openalex.org/W2157748357","https://openalex.org/W2158804744","https://openalex.org/W2170551349","https://openalex.org/W2172966706","https://openalex.org/W2173935179","https://openalex.org/W2182016014","https://openalex.org/W2202810729","https://openalex.org/W2265011897","https://openalex.org/W2344402655","https://openalex.org/W2411162987","https://openalex.org/W2519934224","https://openalex.org/W2535995078","https://openalex.org/W2544757671","https://openalex.org/W2556381003","https://openalex.org/W2560052037","https://openalex.org/W2582257258","https://openalex.org/W2582743722","https://openalex.org/W2605025138","https://openalex.org/W2605533171","https://openalex.org/W2607327662","https://openalex.org/W2615231143","https://openalex.org/W2626532832","https://openalex.org/W2636150609","https://openalex.org/W2688185769","https://openalex.org/W2724836997","https://openalex.org/W2742164178","https://openalex.org/W2742647527","https://openalex.org/W2772418313","https://openalex.org/W2775032901","https://openalex.org/W2775558344","https://openalex.org/W2776526308","https://openalex.org/W2779945812","https://openalex.org/W2782328342","https://openalex.org/W2782696366","https://openalex.org/W2783610221","https://openalex.org/W2784242714","https://openalex.org/W2786808093","https://openalex.org/W2791004613","https://openalex.org/W2793958847","https://openalex.org/W2794830002","https://openalex.org/W2795697644","https://openalex.org/W2802484938","https://openalex.org/W2809677581","https://openalex.org/W2909844436","https://openalex.org/W2921359998","https://openalex.org/W2943796178","https://openalex.org/W2949571567","https://openalex.org/W2950006249","https://openalex.org/W2952002521","https://openalex.org/W2953289982","https://openalex.org/W2966328939","https://openalex.org/W2990305021","https://openalex.org/W3084201551","https://openalex.org/W4229794866","https://openalex.org/W4238719510","https://openalex.org/W4245145908","https://openalex.org/W4247964656","https://openalex.org/W4252500655","https://openalex.org/W4253827031","https://openalex.org/W6632558285","https://openalex.org/W6912748128"],"related_works":["https://openalex.org/W6902031431","https://openalex.org/W6920744002","https://openalex.org/W4400450926","https://openalex.org/W4412523407","https://openalex.org/W4229021641","https://openalex.org/W6931232379","https://openalex.org/W4283825972","https://openalex.org/W4225696641","https://openalex.org/W4211054044","https://openalex.org/W2796038416"],"abstract_inverted_index":{"ABSTRACT":[0],"Background":[1],"The":[2,23,68,218,404],"circular,":[3,176,204,351],"quadripartite":[4,146,177,205,352],"structure":[5,41,147,155,206],"of":[6,19,26,35,56,65,72,98,106,123,138,169,179,195,207,235,243,252,268,312,344,366,386,394,400],"plastid":[7,20,27,39,140,171,181,197,245,259,346,379],"genomes":[8,21,28],"which":[9],"includes":[10],"two":[11,315],"inverted":[12,240,371],"repeat":[13,241,372],"regions":[14,105,242,267],"renders":[15],"the":[16,33,53,63,96,99,135,151,166,180,192,203,208,214,233,239,244,263,310,320,341,364,370,384,397,416],"automatic":[17],"assembly":[18,25,75,83,100,108,142,157,173,199,253,348],"challenging.":[22],"correct":[24],"is":[29,76,162],"a":[30,73,89,117,139,170,175,196,226,256,297,335,345,350,411],"prerequisite":[31],"for":[32,50,82,258,327],"validity":[34],"subsequent":[36],"analyses":[37],"on":[38,111,174,222,314,349],"genome":[40,74,91,141,154,172,198,209,347,380],"and":[42,59,156,230,277,318,355,362,382,410],"evolution.":[43],"Plastome-based":[44],"phylogenetic":[45],"or":[46,120,272],"population":[47],"genetic":[48],"investigations,":[49],"example,":[51],"require":[52],"precise":[54],"identification":[55],"DNA":[57],"sequence":[58],"length":[60],"to":[61,94,202,213,265,279,338,358,377],"determine":[62],"location":[64],"nucleotide":[66],"polymorphisms.":[67],"average":[69],"coverage":[70,86,136,167,193,269,342],"depth":[71,87,137,168,194,270,343],"often":[77],"used":[78],"as":[79,210,212],"an":[80,187,249],"indicator":[81],"quality.":[84,158,254],"Visualizing":[85],"across":[88],"draft":[90],"allows":[92,220],"users":[93,114],"inspect":[95],"quality":[97,306],"and,":[101],"where":[102],"applicable,":[103],"identify":[104,266,280],"reduced":[107],"confidence.":[109],"Based":[110],"such":[112],"visualizations,":[113],"can":[115,133,292],"conduct":[116],"local":[118],"re-assembly":[119],"other":[121],"forms":[122],"targeted":[124],"error":[125],"correction.":[126],"Few,":[127],"if":[128],"any,":[129],"contemporary":[130],"software":[131,160,325,402],"tools":[132,326],"visualize":[134,339],"while":[143],"taking":[144],"its":[145,302],"into":[148,288],"account,":[149],"despite":[150],"interplay":[152],"between":[153],"A":[159],"tool":[161,219,257,337],"needed":[163],"that":[164,190],"visualizes":[165,191,232],"map":[178,354],"genome.":[182],"Results":[183],"We":[184,308],"introduce":[185],"\u2018PACVr\u2019,":[186],"R":[188],"package":[189,417],"in":[200,238,304,356,369,392],"relation":[201,357],"well":[211],"individual":[215,359],"plastome":[216,329,353,360,389],"genes.":[217],"visualizations":[221,322],"different":[223],"scales":[224],"using":[225],"variable":[227],"window":[228],"approach":[229],"also":[231],"equality":[234,365],"gene":[236,367],"synteny":[237,368],"genome,":[246],"thus":[247,300],"providing":[248],"additional":[250],"measure":[251],"As":[255],"genomics,":[260],"PACVr":[261,291,313,333],"provides":[262,334],"functionality":[264],"above":[271],"below":[273],"user-defined":[274],"threshold":[275],"values":[276],"helps":[278],"non-identical":[281],"IR":[282],"regions.":[283,373],"To":[284],"allow":[285],"easy":[286],"integration":[287],"bioinformatic":[289],"workflows,":[290],"be":[293],"directly":[294],"invoked":[295],"from":[296],"Unix":[298],"shell,":[299],"facilitating":[301],"use":[303],"automated":[305],"control.":[307],"illustrate":[309],"application":[311],"empirical":[316],"datasets":[317],"compare":[319],"resulting":[321],"with":[323,415],"alternative":[324,401],"displaying":[328],"sequencing":[330],"coverage.":[331],"Conclusions":[332],"user-friendly":[336],"(a)":[340],"genes,":[361],"(b)":[363],"It,":[374],"thus,":[375],"contributes":[376],"optimizing":[378],"assemblies":[381],"increasing":[383],"reliability":[385],"publicly":[387],"available":[388,414],"sequences,":[390],"especially":[391],"light":[393],"incongruence":[395],"among":[396],"visualization":[398],"results":[399],"tools.":[403],"software,":[405],"example":[406],"datasets,":[407],"technical":[408],"documentation,":[409],"tutorial":[412],"are":[413],"at":[418],"https://github.com/michaelgruenstaeudl/PACVr":[419],".":[420]},"counts_by_year":[{"year":2026,"cited_by_count":42},{"year":2025,"cited_by_count":66},{"year":2024,"cited_by_count":57},{"year":2023,"cited_by_count":63},{"year":2022,"cited_by_count":62},{"year":2021,"cited_by_count":48},{"year":2020,"cited_by_count":4}],"updated_date":"2026-11-05T12:25:35.769452","created_date":"2020-05-29T00:00:00"}
