{"id":"https://openalex.org/W4407248188","doi":"https://doi.org/10.1109/tcbbio.2025.3539629","title":"Quality Scores Compression of Genomic Sequencing Data: A Comprehensive Review and Performance Evaluation","display_name":"Quality Scores Compression of Genomic Sequencing Data: A Comprehensive Review and Performance Evaluation","publication_year":2025,"publication_date":"2025-02-07","ids":{"openalex":"https://openalex.org/W4407248188","doi":"https://doi.org/10.1109/tcbbio.2025.3539629","pmid":"https://pubmed.ncbi.nlm.nih.gov/40811383"},"language":"en","primary_location":{"id":"doi:10.1109/tcbbio.2025.3539629","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3539629","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"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":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5107844343","display_name":"Yuansheng Liu","orcid":"https://orcid.org/0000-0002-7680-3155"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuansheng Liu","raw_affiliation_strings":["College of Information Science and Engineering, Hunan University, Changsha, Hunan, China"],"raw_orcid":"https://orcid.org/0000-0002-7680-3155","affiliations":[{"raw_affiliation_string":"College of Information Science and Engineering, Hunan University, Changsha, Hunan, China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065713846","display_name":"Tao Tang","orcid":"https://orcid.org/0000-0002-1207-4192"},"institutions":[{"id":"https://openalex.org/I41198531","display_name":"Nanjing University of Posts and Telecommunications","ror":"https://ror.org/043bpky34","country_code":"CN","type":"education","lineage":["https://openalex.org/I41198531"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tao Tang","raw_affiliation_strings":["School of Mordern Posts, Nanjing University of Posts and Telecommunications, Nanjing, Jiangsu, China","School of Mordern Posts, Nanjing University of Posts and Telecommunications, Jiangsu, China"],"raw_orcid":"https://orcid.org/0000-0002-1207-4192","affiliations":[{"raw_affiliation_string":"School of Mordern Posts, Nanjing University of Posts and Telecommunications, Nanjing, Jiangsu, China","institution_ids":["https://openalex.org/I41198531"]},{"raw_affiliation_string":"School of Mordern Posts, Nanjing University of Posts and Telecommunications, Jiangsu, China","institution_ids":["https://openalex.org/I41198531"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052762681","display_name":"Zexuan Zhu","orcid":"https://orcid.org/0000-0001-8479-6904"},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zexuan Zhu","raw_affiliation_strings":["College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China"],"raw_orcid":"https://orcid.org/0000-0001-8479-6904","affiliations":[{"raw_affiliation_string":"College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China","institution_ids":["https://openalex.org/I180726961"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Xiangxiang Zeng","orcid":"https://orcid.org/0000-0003-1081-7658"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiangxiang Zeng","raw_affiliation_strings":["College of Information Science and Engineering, Hunan University, Changsha, Hunan, China"],"raw_orcid":"https://orcid.org/0000-0003-1081-7658","affiliations":[{"raw_affiliation_string":"College of Information Science and Engineering, Hunan University, Changsha, Hunan, China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017426085","display_name":"Quan Zou","orcid":"https://orcid.org/0000-0001-6406-1142"},"institutions":[{"id":"https://openalex.org/I150229711","display_name":"University of Electronic Science and Technology of China","ror":"https://ror.org/04qr3zq92","country_code":"CN","type":"education","lineage":["https://openalex.org/I150229711"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Quan Zou","raw_affiliation_strings":["Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China"],"raw_orcid":"https://orcid.org/0000-0001-6406-1142","affiliations":[{"raw_affiliation_string":"Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China","institution_ids":["https://openalex.org/I150229711"]}]},{"author_position":"last","author":{"id":null,"display_name":"Keqin Li","orcid":"https://orcid.org/0000-0001-5224-4048"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Keqin Li","raw_affiliation_strings":["College of Information Science and Engineering, Hunan University, Changsha, Hunan, China"],"raw_orcid":"https://orcid.org/0000-0001-5224-4048","affiliations":[{"raw_affiliation_string":"College of Information Science and Engineering, Hunan University, Changsha, Hunan, China","institution_ids":["https://openalex.org/I16609230"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.483,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.57373672,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"22","issue":"2","first_page":"817","last_page":"831"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.8687000274658203,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.8687000274658203,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/quality","display_name":"Quality (philosophy)","score":0.5021231174468994},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4352295696735382},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4245254397392273},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.36043787002563477},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3271397352218628},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2919875383377075}],"concepts":[{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.5021231174468994},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4352295696735382},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4245254397392273},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.36043787002563477},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3271397352218628},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2919875383377075},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbbio.2025.3539629","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3539629","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"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":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40811383","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40811383","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":"IEEE transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1612661125","display_name":null,"funder_award_id":"2021JJ10020","funder_id":"https://openalex.org/F4320322843","funder_display_name":"Natural Science Foundation of\u00a0Hunan Province"},{"id":"https://openalex.org/G268992786","display_name":null,"funder_award_id":"U22A2037","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3090105490","display_name":null,"funder_award_id":"62272151","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3976198279","display_name":null,"funder_award_id":"62202236","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5477186794","display_name":null,"funder_award_id":"62122025","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5529347993","display_name":null,"funder_award_id":"62102140","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6197502279","display_name":null,"funder_award_id":"62432011","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G635739521","display_name":null,"funder_award_id":"62372159","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G771689064","display_name":null,"funder_award_id":"62450002","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8914552600","display_name":null,"funder_award_id":"62425204","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322843","display_name":"Natural Science Foundation of\u00a0Hunan Province","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":133,"referenced_works":["https://openalex.org/W109642580","https://openalex.org/W783262033","https://openalex.org/W1548134937","https://openalex.org/W1575413654","https://openalex.org/W1647934908","https://openalex.org/W1931027898","https://openalex.org/W1981996205","https://openalex.org/W2006088692","https://openalex.org/W2010928148","https://openalex.org/W2012680439","https://openalex.org/W2020255088","https://openalex.org/W2024143985","https://openalex.org/W2042947822","https://openalex.org/W2046419776","https://openalex.org/W2069066547","https://openalex.org/W2082967074","https://openalex.org/W2083854815","https://openalex.org/W2085522429","https://openalex.org/W2092880969","https://openalex.org/W2097205777","https://openalex.org/W2104846587","https://openalex.org/W2107745473","https://openalex.org/W2108234281","https://openalex.org/W2109153336","https://openalex.org/W2110800670","https://openalex.org/W2111044311","https://openalex.org/W2111451722","https://openalex.org/W2112173167","https://openalex.org/W2112509895","https://openalex.org/W2113649367","https://openalex.org/W2114792961","https://openalex.org/W2116041602","https://openalex.org/W2117608012","https://openalex.org/W2120358246","https://openalex.org/W2123445896","https://openalex.org/W2125557405","https://openalex.org/W2129652681","https://openalex.org/W2130419122","https://openalex.org/W2131694312","https://openalex.org/W2135216100","https://openalex.org/W2137892587","https://openalex.org/W2138196010","https://openalex.org/W2143423077","https://openalex.org/W2146028503","https://openalex.org/W2147492358","https://openalex.org/W2149992227","https://openalex.org/W2150593711","https://openalex.org/W2152073175","https://openalex.org/W2153707226","https://openalex.org/W2158874082","https://openalex.org/W2159084616","https://openalex.org/W2159647614","https://openalex.org/W2159683766","https://openalex.org/W2159906372","https://openalex.org/W2165255717","https://openalex.org/W2168133698","https://openalex.org/W2170551349","https://openalex.org/W2171057071","https://openalex.org/W2269938998","https://openalex.org/W2289678372","https://openalex.org/W2296597603","https://openalex.org/W2339829786","https://openalex.org/W2396849069","https://openalex.org/W2466892528","https://openalex.org/W2486202470","https://openalex.org/W2516970777","https://openalex.org/W2517876513","https://openalex.org/W2531091319","https://openalex.org/W2538355508","https://openalex.org/W2539520752","https://openalex.org/W2560975170","https://openalex.org/W2566058312","https://openalex.org/W2574096291","https://openalex.org/W2597471102","https://openalex.org/W2605012530","https://openalex.org/W2612083776","https://openalex.org/W2616754551","https://openalex.org/W2635555833","https://openalex.org/W2757853464","https://openalex.org/W2764165465","https://openalex.org/W2768268351","https://openalex.org/W2770939534","https://openalex.org/W2771311450","https://openalex.org/W2788946974","https://openalex.org/W2789839305","https://openalex.org/W2885552983","https://openalex.org/W2889470119","https://openalex.org/W2899544675","https://openalex.org/W2905575949","https://openalex.org/W2912135067","https://openalex.org/W2922407406","https://openalex.org/W2937172564","https://openalex.org/W2943420531","https://openalex.org/W2944584631","https://openalex.org/W2946779191","https://openalex.org/W2949113050","https://openalex.org/W2950662571","https://openalex.org/W2951070849","https://openalex.org/W2964849163","https://openalex.org/W2981210020","https://openalex.org/W2991421430","https://openalex.org/W2994713233","https://openalex.org/W2995567032","https://openalex.org/W2998073418","https://openalex.org/W2998688333","https://openalex.org/W3007172120","https://openalex.org/W3011222295","https://openalex.org/W3024135825","https://openalex.org/W3024934024","https://openalex.org/W3031766209","https://openalex.org/W3032570153","https://openalex.org/W3036449824","https://openalex.org/W3036579518","https://openalex.org/W3038162001","https://openalex.org/W3041858939","https://openalex.org/W3042788038","https://openalex.org/W3093528466","https://openalex.org/W3097167873","https://openalex.org/W3098741556","https://openalex.org/W3169629261","https://openalex.org/W3185657184","https://openalex.org/W3186054896","https://openalex.org/W3204360269","https://openalex.org/W3207365242","https://openalex.org/W4200061735","https://openalex.org/W4205177317","https://openalex.org/W4239734004","https://openalex.org/W4281633626","https://openalex.org/W4291281592","https://openalex.org/W4295298624","https://openalex.org/W4323348775","https://openalex.org/W6674561012","https://openalex.org/W6683504902"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"Advanced":[0],"sequencing":[1,13,23,67,80],"technologies":[2],"have":[3],"profoundly":[4],"revolutionized":[5],"biology":[6],"and":[7,31,114,148],"produced":[8],"vast":[9,66],"amounts":[10],"of":[11,22,28,79,116,131,157],"raw":[12],"data":[14,24,29,57],"during":[15],"the":[16,65,76,94,132,154],"past":[17],"decades.":[18],"The":[19],"enormous":[20],"amount":[21],"proposed":[25],"significant":[26],"challenges":[27],"storage":[30],"transmission.":[32],"Compressing":[33],"a":[34,38,128],"big":[35],"file":[36,40],"into":[37],"small":[39],"is":[41],"an":[42,178],"encouraging":[43],"method":[44],"to":[45,88,126,176],"tackle":[46],"these":[47,106,117],"challenges.":[48],"Howver,":[49],"it":[50],"has":[51,85,109],"been":[52,86,110],"found":[53],"that":[54,166],"traditional":[55],"text":[56],"compression":[58,78,103,136,155],"algorithms":[59,71,118,142],"are":[60,72],"not":[61],"well-suited":[62],"for":[63,75,173,181],"handing":[64],"datasets.":[68,163],"Therefore,":[69],"several":[70],"designed":[73],"specifically":[74],"efficient":[77],"data.":[81],"Recently,":[82],"considerable":[83],"research":[84],"devoted":[87],"compressing":[89,182],"quality":[90,134,183],"scores":[91],"stored":[92],"in":[93,99,102],"FASTQ":[95],"format":[96],"file,":[97],"resulting":[98],"substantial":[100],"advances":[101],"performance.":[104],"Despite":[105],"advances,":[107],"there":[108],"no":[111],"systematic":[112],"review":[113,130,168],"evaluation":[115],"or":[119],"software.":[120],"In":[121],"this":[122],"review,":[123],"we":[124,152],"aim":[125],"conduct":[127],"broad":[129],"existing":[133],"score":[135],"algorithms.":[137],"We":[138,164],"mainly":[139],"discuss":[140],"those":[141],"from":[143],"two":[144],"categories,":[145],"i.e.,":[146],"lossless":[147],"lossy":[149],"compression.":[150],"Additionally,":[151],"benchmark":[153],"performance":[156],"12":[158],"tools":[159],"using":[160],"14":[161],"real":[162],"anticipate":[165],"our":[167],"will":[169],"provide":[170],"practical":[171],"guidance":[172],"others":[174],"seeking":[175],"design":[177],"appropriate":[179],"algorithm":[180],"scores.":[184]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-07-15T18:14:33.161393","created_date":"2025-10-10T00:00:00"}
