{"id":"https://openalex.org/W4383199176","doi":"https://doi.org/10.1093/bib/bbad248","title":"From contigs towards chromosomes: automatic improvement of long read assemblies (ILRA)","display_name":"From contigs towards chromosomes: automatic improvement of long read assemblies (ILRA)","publication_year":2023,"publication_date":"2023-06-19","ids":{"openalex":"https://openalex.org/W4383199176","doi":"https://doi.org/10.1093/bib/bbad248","pmid":"https://pubmed.ncbi.nlm.nih.gov/37406192"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbad248","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad248","pdf_url":"https://academic.oup.com/bib/advance-article-pdf/doi/10.1093/bib/bbad248/50825086/bbad248.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in 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/bib/advance-article-pdf/doi/10.1093/bib/bbad248/50825086/bbad248.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100770418","display_name":"Jos\u00e9 Luis Ruiz","orcid":"https://orcid.org/0000-0003-1901-1888"},"institutions":[{"id":"https://openalex.org/I134820265","display_name":"Consejo Superior de Investigaciones Cient\u00edficas","ror":"https://ror.org/02gfc7t72","country_code":"ES","type":"government","lineage":["https://openalex.org/I134820265"]},{"id":"https://openalex.org/I4210153588","display_name":"Instituto de Parasitolog\u00eda y Biomedicina \"L\u00f3pez - Neyra\"","ror":"https://ror.org/05ncvzk72","country_code":"ES","type":"facility","lineage":["https://openalex.org/I134820265","https://openalex.org/I4210153588"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Jos\u00e9 Luis Ruiz","raw_affiliation_strings":["Consejo Superior de Investigaciones Cient\u00edficas Instituto de Parasitolog\u00eda y Biomedicina L\u00f3pez-Neyra (IPBLN), , 18016, Granada , Spain"],"raw_orcid":"https://orcid.org/0000-0003-1901-1888","affiliations":[{"raw_affiliation_string":"Consejo Superior de Investigaciones Cient\u00edficas Instituto de Parasitolog\u00eda y Biomedicina L\u00f3pez-Neyra (IPBLN), , 18016, Granada , Spain","institution_ids":["https://openalex.org/I4210153588","https://openalex.org/I134820265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052811891","display_name":"Susanne Reimering","orcid":"https://orcid.org/0000-0001-8629-0392"},"institutions":[{"id":"https://openalex.org/I4210124929","display_name":"Helmholtz Centre for Infection Research","ror":"https://ror.org/03d0p2685","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I4210124929"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Susanne Reimering","raw_affiliation_strings":["Helmholtz Centre for Infection Research Department for Computational Biology of Infection Research, , Braunschweig , Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Helmholtz Centre for Infection Research Department for Computational Biology of Infection Research, , Braunschweig , Germany","institution_ids":["https://openalex.org/I4210124929"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041137943","display_name":"Juan David Escobar-Prieto","orcid":null},"institutions":[{"id":"https://openalex.org/I4210087692","display_name":"Centro Internacional de Entrenamiento e Investigaciones Medicas","ror":"https://ror.org/003s20294","country_code":"CO","type":"nonprofit","lineage":["https://openalex.org/I4210087692"]}],"countries":["CO"],"is_corresponding":false,"raw_author_name":"Juan David Escobar-Prieto","raw_affiliation_strings":["Centro Internacional de Entrenamiento e Investigaciones M\u00e9dicas (CIDEIM) , Cali , Colombia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centro Internacional de Entrenamiento e Investigaciones M\u00e9dicas (CIDEIM) , Cali , Colombia","institution_ids":["https://openalex.org/I4210087692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080282918","display_name":"Nicolas M. B. Brancucci","orcid":"https://orcid.org/0000-0003-0655-3266"},"institutions":[{"id":"https://openalex.org/I158937107","display_name":"Swiss Tropical and Public Health Institute","ror":"https://ror.org/03adhka07","country_code":"CH","type":"facility","lineage":["https://openalex.org/I158937107"]},{"id":"https://openalex.org/I1850255","display_name":"University of Basel","ror":"https://ror.org/02s6k3f65","country_code":"CH","type":"education","lineage":["https://openalex.org/I1850255"]},{"id":"https://openalex.org/I7882870","display_name":"University of Glasgow","ror":"https://ror.org/00vtgdb53","country_code":"GB","type":"education","lineage":["https://openalex.org/I7882870"]}],"countries":["CH","GB"],"is_corresponding":false,"raw_author_name":"Nicolas M B Brancucci","raw_affiliation_strings":["Swiss Tropical and Public Health Institute Department of Medical Parasitology and Infection Biology, , 4123 Allschwil , Switzerland","University of Basel , 4001 Basel , Switzerland","University of Glasgow School of Infection & Immunity, MVLS, , Glasgow , UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Swiss Tropical and Public Health Institute Department of Medical Parasitology and Infection Biology, , 4123 Allschwil , Switzerland","institution_ids":["https://openalex.org/I158937107"]},{"raw_affiliation_string":"University of Basel , 4001 Basel , Switzerland","institution_ids":["https://openalex.org/I1850255"]},{"raw_affiliation_string":"University of Glasgow School of Infection & Immunity, MVLS, , Glasgow , UK","institution_ids":["https://openalex.org/I7882870"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043866340","display_name":"Diego F. Echeverry","orcid":null},"institutions":[{"id":"https://openalex.org/I4210087692","display_name":"Centro Internacional de Entrenamiento e Investigaciones Medicas","ror":"https://ror.org/003s20294","country_code":"CO","type":"nonprofit","lineage":["https://openalex.org/I4210087692"]},{"id":"https://openalex.org/I91732220","display_name":"Universidad del Valle","ror":"https://ror.org/00jb9vg53","country_code":"CO","type":"education","lineage":["https://openalex.org/I91732220"]}],"countries":["CO"],"is_corresponding":false,"raw_author_name":"Diego F Echeverry","raw_affiliation_strings":["Centro Internacional de Entrenamiento e Investigaciones M\u00e9dicas (CIDEIM) , Cali , Colombia","Universidad del Valle Departamento de Microbiolog\u00eda, Facultad de Salud, , Cali , Colombia"],"raw_orcid":"https://orcid.org/0000-0003-0301-4478","affiliations":[{"raw_affiliation_string":"Centro Internacional de Entrenamiento e Investigaciones M\u00e9dicas (CIDEIM) , Cali , Colombia","institution_ids":["https://openalex.org/I4210087692"]},{"raw_affiliation_string":"Universidad del Valle Departamento de Microbiolog\u00eda, Facultad de Salud, , Cali , Colombia","institution_ids":["https://openalex.org/I91732220"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019859396","display_name":"Abdirahman I. Abdi","orcid":"https://orcid.org/0000-0001-7989-2125"},"institutions":[{"id":"https://openalex.org/I2841861","display_name":"Kenya Medical Research Institute","ror":"https://ror.org/04r1cxt79","country_code":"KE","type":"facility","lineage":["https://openalex.org/I2841861","https://openalex.org/I87048295"]}],"countries":["KE"],"is_corresponding":false,"raw_author_name":"Abdirahman I Abdi","raw_affiliation_strings":["KEMRI-Wellcome Trust Research Programme, CGMRC , Kilifi , Kenya"],"raw_orcid":"https://orcid.org/0000-0001-7989-2125","affiliations":[{"raw_affiliation_string":"KEMRI-Wellcome Trust Research Programme, CGMRC , Kilifi , Kenya","institution_ids":["https://openalex.org/I2841861"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004504354","display_name":"Matthias Marti","orcid":"https://orcid.org/0000-0003-1040-9566"},"institutions":[{"id":"https://openalex.org/I7882870","display_name":"University of Glasgow","ror":"https://ror.org/00vtgdb53","country_code":"GB","type":"education","lineage":["https://openalex.org/I7882870"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Matthias Marti","raw_affiliation_strings":["University of Glasgow School of Infection & Immunity, MVLS, , Glasgow , UK"],"raw_orcid":"https://orcid.org/0000-0003-1040-9566","affiliations":[{"raw_affiliation_string":"University of Glasgow School of Infection & Immunity, MVLS, , Glasgow , UK","institution_ids":["https://openalex.org/I7882870"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028518584","display_name":"Elena G\u00f3mez\u2010D\u00edaz","orcid":"https://orcid.org/0000-0002-4146-9003"},"institutions":[{"id":"https://openalex.org/I134820265","display_name":"Consejo Superior de Investigaciones Cient\u00edficas","ror":"https://ror.org/02gfc7t72","country_code":"ES","type":"government","lineage":["https://openalex.org/I134820265"]},{"id":"https://openalex.org/I4210153588","display_name":"Instituto de Parasitolog\u00eda y Biomedicina \"L\u00f3pez - Neyra\"","ror":"https://ror.org/05ncvzk72","country_code":"ES","type":"facility","lineage":["https://openalex.org/I134820265","https://openalex.org/I4210153588"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Elena G\u00f3mez-D\u00edaz","raw_affiliation_strings":["Consejo Superior de Investigaciones Cient\u00edficas Instituto de Parasitolog\u00eda y Biomedicina L\u00f3pez-Neyra (IPBLN), , 18016, Granada , Spain"],"raw_orcid":"https://orcid.org/0000-0002-4146-9003","affiliations":[{"raw_affiliation_string":"Consejo Superior de Investigaciones Cient\u00edficas Instituto de Parasitolog\u00eda y Biomedicina L\u00f3pez-Neyra (IPBLN), , 18016, Granada , Spain","institution_ids":["https://openalex.org/I4210153588","https://openalex.org/I134820265"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012004257","display_name":"Thomas D. Otto","orcid":"https://orcid.org/0000-0002-1246-7404"},"institutions":[{"id":"https://openalex.org/I7882870","display_name":"University of Glasgow","ror":"https://ror.org/00vtgdb53","country_code":"GB","type":"education","lineage":["https://openalex.org/I7882870"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Thomas D Otto","raw_affiliation_strings":["University of Glasgow School of Infection & Immunity, MVLS, , Glasgow , UK"],"raw_orcid":"https://orcid.org/0000-0002-1246-7404","affiliations":[{"raw_affiliation_string":"University of Glasgow School of Infection & Immunity, MVLS, , Glasgow , UK","institution_ids":["https://openalex.org/I7882870"]}]}],"institutions":[],"countries_distinct_count":6,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5012004257","https://openalex.org/A5100770418"],"corresponding_institution_ids":["https://openalex.org/I134820265","https://openalex.org/I4210153588","https://openalex.org/I7882870"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":3760,"currency":"EUR","value_usd":4055},"fwci":1.8898,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":{"value":0.85732247,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"24","issue":"4","first_page":null,"last_page":null},"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9965000152587891,"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/T10494","display_name":"Plant Virus Research Studies","score":0.9958999752998352,"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/contig","display_name":"Contig","score":0.7474604249000549},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6677173376083374},{"id":"https://openalex.org/keywords/nanopore-sequencing","display_name":"Nanopore sequencing","score":0.6148123741149902},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.611892580986023},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5282511115074158},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.492005318403244},{"id":"https://openalex.org/keywords/sequence-assembly","display_name":"Sequence assembly","score":0.49117395281791687},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4710801839828491},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3772290050983429},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.31787317991256714},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.19203370809555054}],"concepts":[{"id":"https://openalex.org/C59582021","wikidata":"https://www.wikidata.org/wiki/Q1128751","display_name":"Contig","level":4,"score":0.7474604249000549},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6677173376083374},{"id":"https://openalex.org/C126513998","wikidata":"https://www.wikidata.org/wiki/Q8973627","display_name":"Nanopore sequencing","level":4,"score":0.6148123741149902},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.611892580986023},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5282511115074158},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.492005318403244},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.49117395281791687},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4710801839828491},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3772290050983429},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.31787317991256714},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.19203370809555054},{"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/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"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":"D002875","descriptor_name":"Chromosomes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002875","descriptor_name":"Chromosomes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002875","descriptor_name":"Chromosomes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002875","descriptor_name":"Chromosomes","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011544","descriptor_name":"Pseudogenes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011544","descriptor_name":"Pseudogenes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011544","descriptor_name":"Pseudogenes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011544","descriptor_name":"Pseudogenes","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":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1093/bib/bbad248","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad248","pdf_url":"https://academic.oup.com/bib/advance-article-pdf/doi/10.1093/bib/bbad248/50825086/bbad248.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37406192","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37406192","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:digital.csic.es:10261/351318","is_oa":true,"landing_page_url":"http://hdl.handle.net/10261/351318","pdf_url":"https://digital.csic.es/bitstream/10261/351318/1/bbad248.pdf","source":{"id":"https://openalex.org/S4306400616","display_name":"DIGITAL.CSIC (Spanish National Research Council (CSIC))","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I134820265","host_organization_name":"Consejo Superior de Investigaciones Cient\u00edficas","host_organization_lineage":["https://openalex.org/I134820265"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:eprints.gla.ac.uk:303013","is_oa":true,"landing_page_url":null,"pdf_url":"https://eprints.gla.ac.uk/303013/1/303013.pdf","source":{"id":"https://openalex.org/S4210235606","display_name":"ENLIGHTEN (Jurnal Bimbingan dan Konseling Islam)","issn_l":"2622-8912","issn":["2622-8912","2622-8920"],"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-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Articles"},{"id":"pmh:oai:pubmedcentral.nih.gov:10359078","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10359078","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10359078/pdf/bbad248.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbad248","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad248","pdf_url":"https://academic.oup.com/bib/advance-article-pdf/doi/10.1093/bib/bbad248/50825086/bbad248.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3690828678","display_name":null,"funder_award_id":"PID2019","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G3804957094","display_name":null,"funder_award_id":"104111/Z/14/ZR","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G3882965219","display_name":"Elucidating mechanisms of extracellular vesicle-mediated cellular communication and stage conversion in malaria parasites.","funder_award_id":"110166","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G4219695895","display_name":"Wellcome Trust Centre for Molecular Parasitology.","funder_award_id":"104111","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G4501471795","display_name":null,"funder_award_id":"656-2014","funder_id":"https://openalex.org/F4320309955","funder_display_name":"Departamento Administrativo de Ciencia, Tecnolog\u00eda e Innovaci\u00f3n (COLCIENCIAS)"},{"id":"https://openalex.org/G5555687952","display_name":null,"funder_award_id":"FP44842-503-2014","funder_id":"https://openalex.org/F4320309955","funder_display_name":"Departamento Administrativo de Ciencia, Tecnolog\u00eda e Innovaci\u00f3n (COLCIENCIAS)"},{"id":"https://openalex.org/G7818344157","display_name":null,"funder_award_id":"PID2019-111109RB-I00","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G8666890344","display_name":"Wellcome Trust Sanger Institute - generic account for deposition of all core- funded research papers","funder_award_id":"098051","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"}],"funders":[{"id":"https://openalex.org/F4320309955","display_name":"Departamento Administrativo de Ciencia, Tecnolog\u00eda e Innovaci\u00f3n (COLCIENCIAS)","ror":"https://ror.org/048jthh02"},{"id":"https://openalex.org/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"},{"id":"https://openalex.org/F4320312058","display_name":"\u201cla Caixa\u201d Foundation","ror":"https://ror.org/03zhx9h04"},{"id":"https://openalex.org/F4320322930","display_name":"Ministerio de Ciencia e Innovaci\u00f3n","ror":"https://ror.org/034900433"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4383199176.pdf"},"referenced_works_count":55,"referenced_works":["https://openalex.org/W1687604884","https://openalex.org/W1982855075","https://openalex.org/W1983403167","https://openalex.org/W2025583382","https://openalex.org/W2080347313","https://openalex.org/W2099333915","https://openalex.org/W2128964206","https://openalex.org/W2130530163","https://openalex.org/W2132341951","https://openalex.org/W2144883401","https://openalex.org/W2152882637","https://openalex.org/W2155471120","https://openalex.org/W2155628349","https://openalex.org/W2292928167","https://openalex.org/W2338978258","https://openalex.org/W2580040938","https://openalex.org/W2784179637","https://openalex.org/W2799284444","https://openalex.org/W2801980266","https://openalex.org/W2802282671","https://openalex.org/W2805374512","https://openalex.org/W2808052219","https://openalex.org/W2808352813","https://openalex.org/W2897353357","https://openalex.org/W2900054628","https://openalex.org/W2904031666","https://openalex.org/W2912969461","https://openalex.org/W2914685844","https://openalex.org/W2920485215","https://openalex.org/W2929015094","https://openalex.org/W2950354111","https://openalex.org/W2972549919","https://openalex.org/W2992976869","https://openalex.org/W3032077395","https://openalex.org/W3047598142","https://openalex.org/W3085526196","https://openalex.org/W3111384720","https://openalex.org/W3115745540","https://openalex.org/W3128198169","https://openalex.org/W3128727817","https://openalex.org/W3159918988","https://openalex.org/W3163575879","https://openalex.org/W3171794097","https://openalex.org/W3176486499","https://openalex.org/W4213353635","https://openalex.org/W4225268947","https://openalex.org/W4226179456","https://openalex.org/W4281728909","https://openalex.org/W4283809266","https://openalex.org/W4290705484","https://openalex.org/W4315490664","https://openalex.org/W4315707394","https://openalex.org/W4321112378","https://openalex.org/W4322757129","https://openalex.org/W6810582296"],"related_works":["https://openalex.org/W2089480001","https://openalex.org/W2952788979","https://openalex.org/W3009176350","https://openalex.org/W3167837387","https://openalex.org/W2949198880","https://openalex.org/W2763726643","https://openalex.org/W1519765314","https://openalex.org/W3124129973","https://openalex.org/W3005683565","https://openalex.org/W4387503895"],"abstract_inverted_index":{"Recent":[0],"advances":[1],"in":[2],"long":[3,88,189],"read":[4,36,190],"technologies":[5,37],"not":[6],"only":[7],"enable":[8],"large":[9],"consortia":[10],"to":[11,13,25,86,110,163,166,193],"aim":[12],"sequence":[14,26],"all":[15],"eukaryotes":[16],"on":[17],"Earth,":[18],"but":[19,52,158],"they":[20,65],"also":[21],"allow":[22],"individual":[23],"laboratories":[24],"their":[27],"species":[28],"of":[29,41,55,62,124,152,179,187],"interest":[30],"with":[31,46],"relatively":[32],"low":[33,49],"investment.":[34],"Long":[35],"embody":[38],"the":[39,53,60,83,121,150,177,185],"promise":[40],"overcoming":[42],"scaffolding":[43],"problems":[44],"associated":[45],"repeats":[47],"and":[48,64,70,129,132,175],"complexity":[50],"sequences,":[51],"number":[54,61,151],"contigs":[56],"often":[57],"far":[58],"exceeds":[59],"chromosomes":[63],"may":[66],"contain":[67],"many":[68],"insertion":[69],"deletion":[71],"errors":[72],"around":[73],"homopolymer":[74,112,147],"tracts.":[75],"To":[76],"overcome":[77],"these":[78],"issues,":[79],"we":[80,173],"have":[81],"implemented":[82],"ILRA":[84],"pipeline":[85,197],"correct":[87,111,167],"read-based":[89],"assemblies.":[90],"Contigs":[91],"are":[92,107],"first":[93],"reordered,":[94],"renamed,":[95],"merged,":[96],"circularized,":[97],"or":[98,102],"filtered":[99],"if":[100],"erroneous":[101],"contaminated.":[103],"Illumina":[104],"short":[105],"reads":[106],"used":[108],"subsequently":[109],"errors.":[113,170],"We":[114,143],"successfully":[115],"tested":[116],"our":[117,180],"approach":[118,161],"by":[119,133],"improving":[120],"genome":[122],"sequences":[123],"Homo":[125],"sapiens,":[126],"Trypanosoma":[127],"brucei,":[128],"Leptosphaeria":[130],"spp.,":[131],"generating":[134],"four":[135],"novel":[136,188],"Plasmodium":[137],"falciparum":[138],"assemblies":[139,191],"from":[140],"field":[141],"samples.":[142],"found":[144],"that":[145],"correcting":[146],"tracts":[148],"reduced":[149],"genes":[153],"incorrectly":[154],"annotated":[155],"as":[156],"pseudogenes,":[157],"an":[159],"iterative":[160],"seems":[162],"be":[164],"required":[165],"more":[168],"sequencing":[169],"In":[171],"summary,":[172],"describe":[174],"benchmark":[176],"performance":[178],"new":[181],"tool,":[182],"which":[183],"improved":[184],"quality":[186],"up":[192],"1":[194],"Gbp.":[195],"The":[196],"is":[198],"available":[199],"at":[200],"GitHub:":[201],"https://github.com/ThomasDOtto/ILRA.":[202]},"counts_by_year":[{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":3}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
