{"id":"https://openalex.org/W4223993063","doi":"https://doi.org/10.1186/s12859-022-04621-1","title":"BreakAlign: a Perl program to align chimaeric (split) genomic NGS reads and allow visual confirmation of novel retroviral integrations","display_name":"BreakAlign: a Perl program to align chimaeric (split) genomic NGS reads and allow visual confirmation of novel retroviral integrations","publication_year":2022,"publication_date":"2022-04-15","ids":{"openalex":"https://openalex.org/W4223993063","doi":"https://doi.org/10.1186/s12859-022-04621-1","pmid":"https://pubmed.ncbi.nlm.nih.gov/35428171"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-022-04621-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04621-1","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-022-04621-1","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,"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"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-022-04621-1","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5010286627","display_name":"Emanuele Marchi","orcid":"https://orcid.org/0000-0003-1741-9353"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Emanuele Marchi","raw_affiliation_strings":["Nuffield Department of Medicine, University of Oxford, Oxford, UK. emanuele.marchi@ndm.ox.ac.uk","Nuffield Department of Medicine, University of Oxford, Oxford, UK"],"affiliations":[{"raw_affiliation_string":"Nuffield Department of Medicine, University of Oxford, Oxford, UK. emanuele.marchi@ndm.ox.ac.uk","institution_ids":[]},{"raw_affiliation_string":"Nuffield Department of Medicine, University of Oxford, Oxford, UK","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013192404","display_name":"Mathew Jones","orcid":"https://orcid.org/0000-0002-9731-7623"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Mathew Jones","raw_affiliation_strings":["Nuffield Department of Medicine, University of Oxford, Oxford, UK"],"affiliations":[{"raw_affiliation_string":"Nuffield Department of Medicine, University of Oxford, Oxford, UK","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029546143","display_name":"Paul Klenerman","orcid":"https://orcid.org/0000-0003-4307-9161"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Paul Klenerman","raw_affiliation_strings":["Nuffield Department of Medicine, University of Oxford, Oxford, UK"],"affiliations":[{"raw_affiliation_string":"Nuffield Department of Medicine, University of Oxford, Oxford, UK","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044530527","display_name":"John Frater","orcid":"https://orcid.org/0000-0001-7163-7277"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"John Frater","raw_affiliation_strings":["Nuffield Department of Medicine, University of Oxford, Oxford, UK"],"affiliations":[{"raw_affiliation_string":"Nuffield Department of Medicine, University of Oxford, Oxford, UK","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056419497","display_name":"Gkikas Magiorkinis","orcid":"https://orcid.org/0000-0002-0141-4753"},"institutions":[{"id":"https://openalex.org/I200777214","display_name":"National and Kapodistrian University of Athens","ror":"https://ror.org/04gnjpq42","country_code":"GR","type":"education","lineage":["https://openalex.org/I200777214"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Gkikas Magiorkinis","raw_affiliation_strings":["Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece"],"affiliations":[{"raw_affiliation_string":"Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece","institution_ids":["https://openalex.org/I200777214"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5022569324","display_name":"Robert Belshaw","orcid":"https://orcid.org/0000-0001-6234-3947"},"institutions":[{"id":"https://openalex.org/I4210153668","display_name":"Wenzhou-Kean University","ror":"https://ror.org/05609xa16","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210153668"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Robert Belshaw","raw_affiliation_strings":["Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China. rbelshaw@kean.edu","Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China"],"affiliations":[{"raw_affiliation_string":"Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China. rbelshaw@kean.edu","institution_ids":[]},{"raw_affiliation_string":"Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China","institution_ids":["https://openalex.org/I4210153668"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5010286627","https://openalex.org/A5022569324"],"corresponding_institution_ids":["https://openalex.org/I40120149","https://openalex.org/I4210153668"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.4207,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.71586802,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"23","issue":"1","first_page":"134","last_page":"134"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9984999895095825,"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"}},"topics":[{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9984999895095825,"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"}},{"id":"https://openalex.org/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9907000064849854,"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/T10981","display_name":"Cytomegalovirus and herpesvirus research","score":0.972000002861023,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/perl","display_name":"Perl","score":0.7754628658294678},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.674096941947937},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6654859185218811},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.549599289894104},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5447592735290527},{"id":"https://openalex.org/keywords/reference-genome","display_name":"Reference genome","score":0.4114556312561035},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.27303043007850647},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.20231714844703674},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.12659886479377747}],"concepts":[{"id":"https://openalex.org/C2777002779","wikidata":"https://www.wikidata.org/wiki/Q42478","display_name":"Perl","level":2,"score":0.7754628658294678},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.674096941947937},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6654859185218811},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.549599289894104},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5447592735290527},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.4114556312561035},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.27303043007850647},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.20231714844703674},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.12659886479377747}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012190","descriptor_name":"Retroviridae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012190","descriptor_name":"Retroviridae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012190","descriptor_name":"Retroviridae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012190","descriptor_name":"Retroviridae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016662","descriptor_name":"Virus Integration","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016662","descriptor_name":"Virus Integration","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016662","descriptor_name":"Virus Integration","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016662","descriptor_name":"Virus Integration","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-022-04621-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04621-1","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-022-04621-1","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,"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":"pmid:35428171","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35428171","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:f93c3eb8817c4d83a9e60b1652121508","is_oa":true,"landing_page_url":"https://doaj.org/article/f93c3eb8817c4d83a9e60b1652121508","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 23, Iss 1, Pp 1-8 (2022)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9013057","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9013057","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-022-04621-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04621-1","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-022-04621-1","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,"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":[{"display_name":"Good health and well-being","score":0.6299999952316284,"id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G220379493","display_name":null,"funder_award_id":"WT109965MA","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G3528237185","display_name":null,"funder_award_id":"109965MA","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G5053858172","display_name":null,"funder_award_id":"WT109965MA","funder_id":"https://openalex.org/F4320307874","funder_display_name":"Wellcome"},{"id":"https://openalex.org/G5803901190","display_name":null,"funder_award_id":"MR/L006588/1","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G6211367285","display_name":null,"funder_award_id":"109965","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G7099669645","display_name":null,"funder_award_id":"WT109965MA","funder_id":"https://openalex.org/F4320319990","funder_display_name":"National Institute for Health and Care Research"}],"funders":[{"id":"https://openalex.org/F4320307874","display_name":"Wellcome","ror":"https://ror.org/029chgv08"},{"id":"https://openalex.org/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"},{"id":"https://openalex.org/F4320319990","display_name":"National Institute for Health and Care Research","ror":"https://ror.org/0187kwz08"},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"},{"id":"https://openalex.org/F4320336045","display_name":"NIHR Oxford Biomedical Research Centre","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4223993063.pdf","grobid_xml":"https://content.openalex.org/works/W4223993063.grobid-xml"},"referenced_works_count":14,"referenced_works":["https://openalex.org/W2013041617","https://openalex.org/W2033917475","https://openalex.org/W2043248836","https://openalex.org/W2051541780","https://openalex.org/W2114538357","https://openalex.org/W2153689547","https://openalex.org/W2206844597","https://openalex.org/W2267624095","https://openalex.org/W2280129875","https://openalex.org/W2302351081","https://openalex.org/W2305132501","https://openalex.org/W2735027843","https://openalex.org/W2746610802","https://openalex.org/W2997370464"],"related_works":["https://openalex.org/W2921363728","https://openalex.org/W2279684808","https://openalex.org/W3217304749","https://openalex.org/W2066142713","https://openalex.org/W2894932706","https://openalex.org/W2767606877","https://openalex.org/W2582968398","https://openalex.org/W4223446368","https://openalex.org/W4232517363","https://openalex.org/W3214020344"],"abstract_inverted_index":null,"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1}],"updated_date":"2026-03-16T09:10:04.655348","created_date":"2025-10-10T00:00:00"}
