{"id":"https://openalex.org/W4214886535","doi":"https://doi.org/10.5220/0010834100003123","title":"Lossy Compressor Preserving Variant Calling through Extended BWT","display_name":"Lossy Compressor Preserving Variant Calling through Extended BWT","publication_year":2022,"publication_date":"2022-01-01","ids":{"openalex":"https://openalex.org/W4214886535","doi":"https://doi.org/10.5220/0010834100003123"},"language":"en","primary_location":{"id":"doi:10.5220/0010834100003123","is_oa":true,"landing_page_url":"https://doi.org/10.5220/0010834100003123","pdf_url":null,"source":{"id":"https://openalex.org/S4363608833","display_name":"Proceedings of the 15th International Joint Conference on Biomedical Engineering Systems and Technologies","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":"conference"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 15th International Joint Conference on Biomedical Engineering Systems and Technologies","raw_type":"proceedings-article"},"type":"article","indexed_in":["arxiv","crossref"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.5220/0010834100003123","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5091484790","display_name":"Veronica Guerrini","orcid":"https://orcid.org/0000-0001-8888-9243"},"institutions":[{"id":"https://openalex.org/I108290504","display_name":"University of Pisa","ror":"https://ror.org/03ad39j10","country_code":"IT","type":"education","lineage":["https://openalex.org/I108290504"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Veronica Guerrini","raw_affiliation_strings":["Department of Computer Science, University of Pisa, Italy, --- Select a Country ---"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Pisa, Italy, --- Select a Country ---","institution_ids":["https://openalex.org/I108290504"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016168980","display_name":"Felipe A. Louza","orcid":"https://orcid.org/0000-0003-2931-1470"},"institutions":[{"id":"https://openalex.org/I80850581","display_name":"Universidade Federal de Uberl\u00e2ndia","ror":"https://ror.org/04x3wvr31","country_code":"BR","type":"education","lineage":["https://openalex.org/I80850581"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Felipe Louza","raw_affiliation_strings":["Faculty of Electrical Engineering, Federal University of Uberl\u00e2ndia, Brazil, --- Select a Country ---"],"affiliations":[{"raw_affiliation_string":"Faculty of Electrical Engineering, Federal University of Uberl\u00e2ndia, Brazil, --- Select a Country ---","institution_ids":["https://openalex.org/I80850581"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003859151","display_name":"Giovanna Rosone","orcid":"https://orcid.org/0000-0001-5075-1214"},"institutions":[{"id":"https://openalex.org/I108290504","display_name":"University of Pisa","ror":"https://ror.org/03ad39j10","country_code":"IT","type":"education","lineage":["https://openalex.org/I108290504"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Giovanna Rosone","raw_affiliation_strings":["Department of Computer Science, University of Pisa, Italy, --- Select a Country ---"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Pisa, Italy, --- Select a Country ---","institution_ids":["https://openalex.org/I108290504"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5091484790"],"corresponding_institution_ids":["https://openalex.org/I108290504"],"apc_list":null,"apc_paid":null,"fwci":0.2087,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.37472178,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":96},"biblio":{"volume":null,"issue":null,"first_page":"38","last_page":"48"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9990000128746033,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9855999946594238,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8705002069473267},{"id":"https://openalex.org/keywords/lossy-compression","display_name":"Lossy compression","score":0.7744916081428528},{"id":"https://openalex.org/keywords/redundancy","display_name":"Redundancy (engineering)","score":0.7263516783714294},{"id":"https://openalex.org/keywords/encoding","display_name":"Encoding (memory)","score":0.5129818320274353},{"id":"https://openalex.org/keywords/data-compression","display_name":"Data compression","score":0.4953650236129761},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.47081097960472107},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.4495854377746582},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.15762794017791748},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.08266308903694153}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8705002069473267},{"id":"https://openalex.org/C165021410","wikidata":"https://www.wikidata.org/wiki/Q55564","display_name":"Lossy compression","level":2,"score":0.7744916081428528},{"id":"https://openalex.org/C152124472","wikidata":"https://www.wikidata.org/wiki/Q1204361","display_name":"Redundancy (engineering)","level":2,"score":0.7263516783714294},{"id":"https://openalex.org/C125411270","wikidata":"https://www.wikidata.org/wiki/Q18653","display_name":"Encoding (memory)","level":2,"score":0.5129818320274353},{"id":"https://openalex.org/C78548338","wikidata":"https://www.wikidata.org/wiki/Q2493","display_name":"Data compression","level":2,"score":0.4953650236129761},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.47081097960472107},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.4495854377746582},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.15762794017791748},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.08266308903694153}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.5220/0010834100003123","is_oa":true,"landing_page_url":"https://doi.org/10.5220/0010834100003123","pdf_url":null,"source":{"id":"https://openalex.org/S4363608833","display_name":"Proceedings of the 15th International Joint Conference on Biomedical Engineering Systems and Technologies","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":"conference"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 15th International Joint Conference on Biomedical Engineering Systems and Technologies","raw_type":"proceedings-article"},{"id":"pmh:oai:arXiv.org:2304.08534","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2304.08534","pdf_url":"https://arxiv.org/pdf/2304.08534","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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":null,"raw_type":"text"},{"id":"pmh:oai:arpi.unipi.it:11568/1130518","is_oa":false,"landing_page_url":"http://hdl.handle.net/11568/1130518","pdf_url":null,"source":{"id":"https://openalex.org/S4377196265","display_name":"CINECA IRIS Institutial research information system (University of Pisa)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I108290504","host_organization_name":"University of Pisa","host_organization_lineage":["https://openalex.org/I108290504"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/conferenceObject"}],"best_oa_location":{"id":"doi:10.5220/0010834100003123","is_oa":true,"landing_page_url":"https://doi.org/10.5220/0010834100003123","pdf_url":null,"source":{"id":"https://openalex.org/S4363608833","display_name":"Proceedings of the 15th International Joint Conference on Biomedical Engineering Systems and Technologies","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":"conference"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 15th International Joint Conference on Biomedical Engineering Systems and Technologies","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1121067466","display_name":null,"funder_award_id":"PRA_2020-2021_2","funder_id":"https://openalex.org/F4320324499","funder_display_name":"Universit\u00e0 di Pisa"},{"id":"https://openalex.org/G1343878812","display_name":null,"funder_award_id":"RBSI146R5L","funder_id":"https://openalex.org/F4320321873","funder_display_name":"Ministero dell\u2019Istruzione, dell\u2019Universit\u00e0 e della Ricerca"},{"id":"https://openalex.org/G1985916764","display_name":null,"funder_award_id":"Ateneo_","funder_id":"https://openalex.org/F4320324499","funder_display_name":"Universit\u00e0 di Pisa"},{"id":"https://openalex.org/G4300441511","display_name":null,"funder_award_id":"PRA_2020-2021_26","funder_id":"https://openalex.org/F4320324499","funder_display_name":"Universit\u00e0 di Pisa"},{"id":"https://openalex.org/G4480700526","display_name":null,"funder_award_id":"PRA_2020-2021","funder_id":"https://openalex.org/F4320324499","funder_display_name":"Universit\u00e0 di Pisa"},{"id":"https://openalex.org/G8175194624","display_name":null,"funder_award_id":"PRA 2020","funder_id":"https://openalex.org/F4320324499","funder_display_name":"Universit\u00e0 di Pisa"}],"funders":[{"id":"https://openalex.org/F4320321873","display_name":"Ministero dell\u2019Istruzione, dell\u2019Universit\u00e0 e della Ricerca","ror":"https://ror.org/0166hxq48"},{"id":"https://openalex.org/F4320324499","display_name":"Universit\u00e0 di Pisa","ror":"https://ror.org/03ad39j10"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":40,"referenced_works":["https://openalex.org/W1488229309","https://openalex.org/W1931027898","https://openalex.org/W1969173824","https://openalex.org/W1987760161","https://openalex.org/W2051511420","https://openalex.org/W2069066547","https://openalex.org/W2076359272","https://openalex.org/W2081423260","https://openalex.org/W2086782013","https://openalex.org/W2092880969","https://openalex.org/W2102987669","https://openalex.org/W2111044311","https://openalex.org/W2125557405","https://openalex.org/W2131106408","https://openalex.org/W2134283755","https://openalex.org/W2135771747","https://openalex.org/W2143423077","https://openalex.org/W2158322625","https://openalex.org/W2161628678","https://openalex.org/W2168133698","https://openalex.org/W2296597603","https://openalex.org/W2466892528","https://openalex.org/W2538355508","https://openalex.org/W2739364690","https://openalex.org/W2905575949","https://openalex.org/W2919789042","https://openalex.org/W2920034498","https://openalex.org/W2947183814","https://openalex.org/W2963995493","https://openalex.org/W2991421430","https://openalex.org/W2998912266","https://openalex.org/W2999295646","https://openalex.org/W3010768629","https://openalex.org/W3087467602","https://openalex.org/W3087625265","https://openalex.org/W3089043377","https://openalex.org/W3102885865","https://openalex.org/W3203859541","https://openalex.org/W4247053599","https://openalex.org/W4394666350"],"related_works":["https://openalex.org/W2547124190","https://openalex.org/W2385628723","https://openalex.org/W2888954728","https://openalex.org/W2552401318","https://openalex.org/W108076602","https://openalex.org/W3180760233","https://openalex.org/W4384342390","https://openalex.org/W3035703949","https://openalex.org/W4247601675","https://openalex.org/W1033938421"],"abstract_inverted_index":{"A":[0],"standard":[1],"format":[2],"used":[3,34,53],"for":[4,35,54],"storing":[5],"the":[6,13,68,73,76,84,101,106,110,119,141,163,165],"output":[7],"of":[8,87,109],"high-throughput":[9],"sequencing":[10,39],"experiments":[11],"is":[12,148,167],"FASTQ":[14,65,94],"format.":[15],"It":[16],"comprises":[17],"three":[18],"main":[19],"components:":[20],"(i)":[21],"headers,":[22],"(ii)":[23],"bases":[24,74],"(nucleotide":[25],"sequences),":[26],"and":[27,124,127,135],"(iii)":[28],"quality":[29,77],"scores.&#13;\\nFASTQ":[30],"files":[31],"are":[32,41,57],"widely":[33],"variant":[36,159],"calling,":[37],"where":[38],"data":[40,66,95],"mapped":[42],"into":[43],"a":[44,91,114],"reference":[45],"genome":[46],"to":[47,150,158],"discover":[48],"variants":[49],"that":[50,61,140],"may":[51],"be":[52],"further":[55],"analysis.&#13;\\nThere":[56],"many":[58],"specialized":[59],"compressors":[60],"exploit":[62],"redundancy":[63],"in":[64,90,131],"with":[67],"focus":[69],"only":[70],"on":[71,118],"either":[72],"or":[75],"scores":[78],"components.&#13;\\nIn":[79],"this":[80],"paper":[81],"we":[82,128],"consider":[83],"novel":[85],"problem":[86],"lossy":[88,142],"compressing,":[89],"reference-free":[92],"way,":[93],"by":[96,145],"modifying":[97],"both":[98,132],"components":[99],"at":[100,170],"same":[102],"time,":[103],"while":[104,154],"preserving":[105,155],"important":[107],"information":[108,156],"original":[111],"FASTQ.&#13;\\nWe":[112],"introduce":[113],"general":[115],"strategy,":[116],"based":[117],"Extended":[120],"Burrows-Wheeler":[121],"Transform":[122],"(EBWT)":[123],"positional":[125],"clustering,":[126],"present":[129],"implementations":[130],"internal":[133],"memory":[134],"external":[136],"memory.&#13;\\nExperimental":[137],"results":[138],"show":[139],"compression":[143,153],"performed":[144],"our":[146],"tool":[147],"able":[149],"achieve":[151],"good":[152],"relating":[157],"calling":[160],"more":[161],"than":[162],"competitors.&#13;\\n&#13;\\nAvailability:":[164],"software":[166],"freely":[168],"available":[169],"https://github.com/veronicaguerrini/BFQzip.":[171]},"counts_by_year":[{"year":2023,"cited_by_count":2}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
