{"id":"https://openalex.org/W2888657712","doi":"https://doi.org/10.1093/bioinformatics/bty745","title":"RepeatCraft: a meta-pipeline for repetitive element de-fragmentation and annotation","display_name":"RepeatCraft: a meta-pipeline for repetitive element de-fragmentation and annotation","publication_year":2018,"publication_date":"2018-08-23","ids":{"openalex":"https://openalex.org/W2888657712","doi":"https://doi.org/10.1093/bioinformatics/bty745","mag":"2888657712","pmid":"https://pubmed.ncbi.nlm.nih.gov/30165587"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty745","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty745","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/6/1051/28079171/bty745.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/35/6/1051/28079171/bty745.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5025039691","display_name":"Wai Yee Wong","orcid":"https://orcid.org/0000-0002-2329-2566"},"institutions":[{"id":"https://openalex.org/I129774422","display_name":"University of Vienna","ror":"https://ror.org/03prydq77","country_code":"AT","type":"education","lineage":["https://openalex.org/I129774422"]}],"countries":["AT"],"is_corresponding":true,"raw_author_name":"Wai Yee Wong","raw_affiliation_strings":["Department of Molecular Evolution and Development, Faculty of Life Science, University of Vienna, A-1090 Vienna, Austria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Evolution and Development, Faculty of Life Science, University of Vienna, A-1090 Vienna, Austria","institution_ids":["https://openalex.org/I129774422"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5041816560","display_name":"Oleg Simakov","orcid":"https://orcid.org/0000-0002-3585-4511"},"institutions":[{"id":"https://openalex.org/I129774422","display_name":"University of Vienna","ror":"https://ror.org/03prydq77","country_code":"AT","type":"education","lineage":["https://openalex.org/I129774422"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Oleg Simakov","raw_affiliation_strings":["Department of Molecular Evolution and Development, Faculty of Life Science, University of Vienna, A-1090 Vienna, Austria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Evolution and Development, Faculty of Life Science, University of Vienna, A-1090 Vienna, Austria","institution_ids":["https://openalex.org/I129774422"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5025039691"],"corresponding_institution_ids":["https://openalex.org/I129774422"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":{"value":3989,"currency":"USD","value_usd":3989},"fwci":0.6617,"has_fulltext":true,"cited_by_count":61,"citation_normalized_percentile":{"value":0.67138026,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":93,"max":100},"biblio":{"volume":"35","issue":"6","first_page":"1051","last_page":"1052"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.7282000184059143,"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":0.7282000184059143,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.0502999983727932,"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/T10949","display_name":"Genetic Neurodegenerative Diseases","score":0.04690000042319298,"subfield":{"id":"https://openalex.org/subfields/2804","display_name":"Cellular and Molecular Neuroscience"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.7374199032783508},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.6637861728668213},{"id":"https://openalex.org/keywords/fragmentation","display_name":"Fragmentation (computing)","score":0.6427561640739441},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6117337942123413},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.1878400444984436},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.15268349647521973}],"concepts":[{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.7374199032783508},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6637861728668213},{"id":"https://openalex.org/C191015642","wikidata":"https://www.wikidata.org/wiki/Q1132459","display_name":"Fragmentation (computing)","level":2,"score":0.6427561640739441},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6117337942123413},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1878400444984436},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.15268349647521973}],"mesh":[{"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":"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":"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":"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},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064878","descriptor_name":"Web Browser","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064878","descriptor_name":"Web Browser","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064878","descriptor_name":"Web Browser","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064878","descriptor_name":"Web Browser","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064878","descriptor_name":"Web Browser","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/bty745","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty745","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/6/1051/28079171/bty745.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","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:30165587","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30165587","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":"Journal Article"},{"id":"pmh:oai:europepmc.org:5408841","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC6419915","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:6419915","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6419915","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,"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"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty745","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty745","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/6/1051/28079171/bty745.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","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/G5932169686","display_name":null,"funder_award_id":"P30686\u2010B29)","funder_id":"https://openalex.org/F4320321181","funder_display_name":"Austrian Science Fund"},{"id":"https://openalex.org/G7523241304","display_name":"Genome dynamics in cephalopods and their functional impact","funder_award_id":"P30686","funder_id":"https://openalex.org/F4320321181","funder_display_name":"Austrian Science Fund"}],"funders":[{"id":"https://openalex.org/F4320321181","display_name":"Austrian Science Fund","ror":"https://ror.org/013tf3c58"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2888657712.pdf","grobid_xml":"https://content.openalex.org/works/W2888657712.grobid-xml"},"referenced_works_count":6,"referenced_works":["https://openalex.org/W1990645521","https://openalex.org/W2031493923","https://openalex.org/W2073915279","https://openalex.org/W2082330286","https://openalex.org/W2106736840","https://openalex.org/W2142466527"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2361861616","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2218034408","https://openalex.org/W2392921965","https://openalex.org/W2358755282","https://openalex.org/W2625833328"],"abstract_inverted_index":{"SUMMARY:":[0],"Repetitive":[1],"elements":[2],"comprise":[3],"large":[4],"proportion":[5],"of":[6,23,51,61,138],"many":[7,52],"genomes.":[8,41],"They":[9],"have":[10],"impact":[11],"on":[12,71,88],"both":[13,89],"genome":[14],"evolution":[15],"and":[16,20,37,64,92,114,136,150,159],"regulation.":[17],"Their":[18],"classification":[19,60,85],"the":[21,48,59,103,139,151],"study":[22],"evolutionary":[24,66],"history":[25],"is":[26,47,146,154,161],"a":[27,75,111,121,128],"major":[28,43],"emerging":[29],"field.":[30],"Various":[31],"software":[32],"exist":[33],"to-date":[34],"to":[35],"classify":[36],"map":[38],"repeats":[39,63],"across":[40],"The":[42,95,117],"unresolved":[44],"drawback,":[45],"however,":[46],"fragmented":[49],"nature":[50],"identified":[53],"repeat":[54,83,100,140],"loci.":[55],"This":[56],"ultimately":[57],"makes":[58],"novel":[62],"their":[65],"analyses":[67],"difficult.":[68],"To":[69],"improve":[70],"this,":[72],"we":[73],"developed":[74],"pipeline":[76,96,118],"(RepeatCraft)":[77],"that":[78,124],"integrates":[79],"results":[80],"from":[81],"several":[82],"element":[84],"tools":[86],"based":[87],"sequence":[90,115],"similarity":[91],"structural":[93],"features.":[94],"de-fragments":[97],"closely":[98],"spaced":[99],"loci":[101],"in":[102,127,148,156],"genomes,":[104],"reconstructing":[105],"longer":[106],"copies,":[107],"thus":[108],"allowing":[109,131],"for":[110,132],"better":[112],"annotation":[113],"comparisons.":[116],"also":[119],"includes":[120],"user":[122],"interface":[123],"can":[125],"run":[126],"web":[129,152],"browser":[130],"an":[133],"easy":[134],"access":[135],"exploration":[137],"data.":[141],"AVAILABILITY":[142],"AND":[143],"IMPLEMENTATION:":[144],"RepeatCraft":[145],"implemented":[147,155],"Python":[149],"application":[153],"R.":[157],"Download":[158],"documentation":[160],"freely":[162],"available":[163,171],"at":[164,172],"https://github.com/niccw/repeatCraftp.":[165],"SUPPLEMENTARY":[166],"INFORMATION:":[167],"Supplementary":[168],"data":[169],"are":[170],"Bioinformatics":[173],"online.":[174]},"counts_by_year":[{"year":2026,"cited_by_count":10},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":24},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":2}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
