{"id":"https://openalex.org/W3124386847","doi":"https://doi.org/10.1186/s40537-021-00418-w","title":"CaReAl: capturing read alignments in a BAM file rapidly and conveniently","display_name":"CaReAl: capturing read alignments in a BAM file rapidly and conveniently","publication_year":2021,"publication_date":"2021-01-26","ids":{"openalex":"https://openalex.org/W3124386847","doi":"https://doi.org/10.1186/s40537-021-00418-w","mag":"3124386847"},"language":"en","primary_location":{"id":"doi:10.1186/s40537-021-00418-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s40537-021-00418-w","pdf_url":"https://journalofbigdata.springeropen.com/track/pdf/10.1186/s40537-021-00418-w","source":{"id":"https://openalex.org/S2737955091","display_name":"Journal Of Big Data","issn_l":"2196-1115","issn":["2196-1115"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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":"Journal of Big Data","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journalofbigdata.springeropen.com/track/pdf/10.1186/s40537-021-00418-w","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101441836","display_name":"Yoomi Park","orcid":"https://orcid.org/0000-0002-5953-0378"},"institutions":[{"id":"https://openalex.org/I139264467","display_name":"Seoul National University","ror":"https://ror.org/04h9pn542","country_code":"KR","type":"education","lineage":["https://openalex.org/I139264467"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Yoomi Park","raw_affiliation_strings":["Div. of Biomedical Informatics, Seoul National University College of Medicine, Seoul National University Biomedical Informatics (SNUBI), Seoul, Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Div. of Biomedical Informatics, Seoul National University College of Medicine, Seoul National University Biomedical Informatics (SNUBI), Seoul, Korea","institution_ids":["https://openalex.org/I139264467"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000906400","display_name":"Heewon Seo","orcid":"https://orcid.org/0000-0001-6218-8609"},"institutions":[{"id":"https://openalex.org/I1325899441","display_name":"University Health Network","ror":"https://ror.org/042xt5161","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1325899441"]},{"id":"https://openalex.org/I139264467","display_name":"Seoul National University","ror":"https://ror.org/04h9pn542","country_code":"KR","type":"education","lineage":["https://openalex.org/I139264467"]},{"id":"https://openalex.org/I2802654988","display_name":"Princess Margaret Cancer Centre","ror":"https://ror.org/03zayce58","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1325899441","https://openalex.org/I2802654988"]}],"countries":["CA","KR"],"is_corresponding":false,"raw_author_name":"Heewon Seo","raw_affiliation_strings":["Div. of Biomedical Informatics, Seoul National University College of Medicine, Seoul National University Biomedical Informatics (SNUBI), Seoul, Korea","Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Div. of Biomedical Informatics, Seoul National University College of Medicine, Seoul National University Biomedical Informatics (SNUBI), Seoul, Korea","institution_ids":["https://openalex.org/I139264467"]},{"raw_affiliation_string":"Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada","institution_ids":["https://openalex.org/I1325899441","https://openalex.org/I2802654988"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022047971","display_name":"Kyung Hun Yoo","orcid":"https://orcid.org/0000-0003-2250-5280"},"institutions":[{"id":"https://openalex.org/I139264467","display_name":"Seoul National University","ror":"https://ror.org/04h9pn542","country_code":"KR","type":"education","lineage":["https://openalex.org/I139264467"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Kyunghun Yoo","raw_affiliation_strings":["Div. of Biomedical Informatics, Seoul National University College of Medicine, Seoul National University Biomedical Informatics (SNUBI), Seoul, Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Div. of Biomedical Informatics, Seoul National University College of Medicine, Seoul National University Biomedical Informatics (SNUBI), Seoul, Korea","institution_ids":["https://openalex.org/I139264467"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101730979","display_name":"Ju Han Kim","orcid":"https://orcid.org/0000-0003-1522-9038"},"institutions":[{"id":"https://openalex.org/I139264467","display_name":"Seoul National University","ror":"https://ror.org/04h9pn542","country_code":"KR","type":"education","lineage":["https://openalex.org/I139264467"]},{"id":"https://openalex.org/I2802835388","display_name":"Seoul National University Hospital","ror":"https://ror.org/01z4nnt86","country_code":"KR","type":"healthcare","lineage":["https://openalex.org/I139264467","https://openalex.org/I2802835388"]}],"countries":["KR"],"is_corresponding":true,"raw_author_name":"Ju Han Kim","raw_affiliation_strings":["Center for Precision Medicine, Seoul National University Hospital, Seoul, Korea","Div. of Biomedical Informatics, Seoul National University College of Medicine, Seoul National University Biomedical Informatics (SNUBI), Seoul, Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Precision Medicine, Seoul National University Hospital, Seoul, Korea","institution_ids":["https://openalex.org/I2802835388"]},{"raw_affiliation_string":"Div. of Biomedical Informatics, Seoul National University College of Medicine, Seoul National University Biomedical Informatics (SNUBI), Seoul, Korea","institution_ids":["https://openalex.org/I139264467"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5101730979"],"corresponding_institution_ids":["https://openalex.org/I139264467","https://openalex.org/I2802835388"],"apc_list":{"value":1570,"currency":"USD","value_usd":1570},"apc_paid":{"value":1570,"currency":"USD","value_usd":1570},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.00510187,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"8","issue":"1","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":1.0,"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":1.0,"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":0.9965999722480774,"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":0.9847000241279602,"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/computer-science","display_name":"Computer science","score":0.8624738454818726},{"id":"https://openalex.org/keywords/snapshot","display_name":"Snapshot (computer storage)","score":0.8229667544364929},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.7011428475379944},{"id":"https://openalex.org/keywords/multithreading","display_name":"Multithreading","score":0.660963773727417},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4535447657108307},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.20044195652008057},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.19191387295722961},{"id":"https://openalex.org/keywords/thread","display_name":"Thread (computing)","score":0.1004195511341095}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8624738454818726},{"id":"https://openalex.org/C55282118","wikidata":"https://www.wikidata.org/wiki/Q252683","display_name":"Snapshot (computer storage)","level":2,"score":0.8229667544364929},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.7011428475379944},{"id":"https://openalex.org/C201410400","wikidata":"https://www.wikidata.org/wiki/Q1064412","display_name":"Multithreading","level":3,"score":0.660963773727417},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4535447657108307},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.20044195652008057},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.19191387295722961},{"id":"https://openalex.org/C138101251","wikidata":"https://www.wikidata.org/wiki/Q213092","display_name":"Thread (computing)","level":2,"score":0.1004195511341095}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/s40537-021-00418-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s40537-021-00418-w","pdf_url":"https://journalofbigdata.springeropen.com/track/pdf/10.1186/s40537-021-00418-w","source":{"id":"https://openalex.org/S2737955091","display_name":"Journal Of Big Data","issn_l":"2196-1115","issn":["2196-1115"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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":"Journal of Big Data","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:000477a9471e46e58b9561ffa50fc74c","is_oa":true,"landing_page_url":"https://doaj.org/article/000477a9471e46e58b9561ffa50fc74c","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,"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":"Journal of Big Data, Vol 8, Iss 1, Pp 1-8 (2021)","raw_type":"article"},{"id":"pmh:oai:s-space.snu.ac.kr:10371/173895","is_oa":false,"landing_page_url":"https://hdl.handle.net/10371/173895","pdf_url":null,"source":{"id":"https://openalex.org/S4306401345","display_name":"Seoul National University Open Repository (Seoul National University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139264467","host_organization_name":"Seoul National University","host_organization_lineage":["https://openalex.org/I139264467"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1186/s40537-021-00418-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s40537-021-00418-w","pdf_url":"https://journalofbigdata.springeropen.com/track/pdf/10.1186/s40537-021-00418-w","source":{"id":"https://openalex.org/S2737955091","display_name":"Journal Of Big Data","issn_l":"2196-1115","issn":["2196-1115"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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":"Journal of Big Data","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G8327154243","display_name":null,"funder_award_id":"16183MFDS541","funder_id":"https://openalex.org/F4320322014","funder_display_name":"Ministry of Food and Drug Safety"},{"id":"https://openalex.org/G844139613","display_name":null,"funder_award_id":"16183MFDS541","funder_id":"https://openalex.org/F4320334878","funder_display_name":"National Institute of Food and Drug Safety Evaluation"}],"funders":[{"id":"https://openalex.org/F4320322014","display_name":"Ministry of Food and Drug Safety","ror":"https://ror.org/01f7dp456"},{"id":"https://openalex.org/F4320334878","display_name":"National Institute of Food and Drug Safety Evaluation","ror":"https://ror.org/027k9sa32"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3124386847.pdf","grobid_xml":"https://content.openalex.org/works/W3124386847.grobid-xml"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W1490553060","https://openalex.org/W1577822803","https://openalex.org/W1882576502","https://openalex.org/W1971584645","https://openalex.org/W1995078504","https://openalex.org/W2087008771","https://openalex.org/W2087464200","https://openalex.org/W2101016096","https://openalex.org/W2105368763","https://openalex.org/W2108234281","https://openalex.org/W2117131162","https://openalex.org/W2122270655","https://openalex.org/W2136661588","https://openalex.org/W2142386149","https://openalex.org/W2148683465","https://openalex.org/W2170488656","https://openalex.org/W2176699305","https://openalex.org/W2252255302","https://openalex.org/W2295828257","https://openalex.org/W2736370284","https://openalex.org/W2919717584","https://openalex.org/W2940391028","https://openalex.org/W3007907037","https://openalex.org/W3016096434"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W1940589050","https://openalex.org/W2355721938","https://openalex.org/W2387608311","https://openalex.org/W2973764441","https://openalex.org/W2542847180","https://openalex.org/W2086248387","https://openalex.org/W196517846"],"abstract_inverted_index":{"Abstract":[0],"Some":[1],"of":[2,49,67,81,83,93,113,141,150,174],"the":[3,16,47,64,78,104,144,172],"variants":[4],"detected":[5],"by":[6,85],"high-throughput":[7],"sequencing":[8],"(HTS)":[9],"are":[10],"often":[11],"not":[12],"reproducible.":[13],"To":[14],"minimize":[15],"technical-induced":[17],"artifacts,":[18],"secondary":[19],"experimental":[20],"validation":[21],"is":[22,27,42,75,121,158],"required":[23],"but":[24],"this":[25],"step":[26],"unnecessarily":[28],"slow":[29],"and":[30,36,70,131,137,148,154,161],"expensive.":[31],"Thus,":[32],"developing":[33],"a":[34,56,91,159],"rapid":[35,117,160],"easy":[37],"to":[38,44],"use":[39],"visualization":[40],"tool":[41,107,120,163],"necessary":[43],"systematically":[45],"review":[46,147],"statuses":[48,89],"sequence":[50,114,152],"read":[51],"alignments.":[52],"Here,":[53],"we":[54],"developed":[55],"high-performance":[57],"alignment":[58],"capturing":[59,119,165],"tool,":[60],"CaReAl,":[61],"for":[62,77,123,127,164,178],"visualizing":[63,86],"read-alignment":[65,88],"status":[66],"nucleotide":[68],"sequences":[69],"associated":[71],"genome":[72,151],"features.":[73],"CaReAl":[74,96,142,157,170],"optimized":[76],"systematic":[79],"exploration":[80],"regions":[82],"interest":[84],"full-depth":[87],"in":[90,168],"set":[92],"PNG":[94],"files.":[95],"was":[97],"7.5":[98],"times":[99],"faster":[100],"than":[101],"IGV":[102],"\u2018snapshot\u2019,":[103],"only":[105],"stand-alone":[106],"which":[108],"provides":[109],"an":[110],"automated":[111],"snapshot":[112],"reads.":[115],"This":[116],"user-programmable":[118],"useful":[122],"obtaining":[124,179],"read-level":[125],"data":[126,177],"evaluating":[128],"variant":[129,155],"calls":[130],"detecting":[132],"technical":[133],"biases.":[134],"The":[135],"multithreading":[136],"sequential":[138],"wide-genome-range-capturing":[139],"functionalities":[140],"aid":[143],"efficient":[145],"manual":[146],"evaluation":[149],"alignments":[153],"calls.":[156],"convenient":[162],"aligned":[166],"reads":[167],"BAM.":[169],"facilitates":[171],"acquisition":[173],"highly":[175],"curated":[176],"reliable":[180],"analytic":[181],"results.":[182]},"counts_by_year":[],"updated_date":"2026-08-28T12:50:07.497085","created_date":"2025-10-10T00:00:00"}
