{"id":"https://openalex.org/W2911891532","doi":"https://doi.org/10.1109/bibm.2018.8621573","title":"Performance Evaluation of IMP: A Rapid Secondary Analysis Pipeline for NGS Data","display_name":"Performance Evaluation of IMP: A Rapid Secondary Analysis Pipeline for NGS Data","publication_year":2018,"publication_date":"2018-12-01","ids":{"openalex":"https://openalex.org/W2911891532","doi":"https://doi.org/10.1109/bibm.2018.8621573","mag":"2911891532"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2018.8621573","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2018.8621573","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5102163014","display_name":"Shun Wang","orcid":"https://orcid.org/0009-0003-8985-7157"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Shun Wang","raw_affiliation_strings":["Aginome Scientific, China"],"affiliations":[{"raw_affiliation_string":"Aginome Scientific, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062411566","display_name":"Wenxian Yang","orcid":"https://orcid.org/0000-0002-5349-9680"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wenxian Yang","raw_affiliation_strings":["Aginome Scientific, China"],"affiliations":[{"raw_affiliation_string":"Aginome Scientific, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052625301","display_name":"Xiang Zhang","orcid":"https://orcid.org/0000-0002-0827-9443"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Xiang Zhang","raw_affiliation_strings":["Aginome Scientific, China"],"affiliations":[{"raw_affiliation_string":"Aginome Scientific, China","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5068270780","display_name":"Rongshan Yu","orcid":"https://orcid.org/0000-0003-2179-173X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Rongshan Yu","raw_affiliation_strings":["Aginome Scientific, China"],"affiliations":[{"raw_affiliation_string":"Aginome Scientific, China","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5102163014"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0919,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.49215729,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"32","issue":null,"first_page":"1170","last_page":"1176"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.996999979019165,"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":0.996999979019165,"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.994700014591217,"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"}},{"id":"https://openalex.org/T11181","display_name":"Advanced Data Storage Technologies","score":0.9850999712944031,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.804803729057312},{"id":"https://openalex.org/keywords/bottleneck","display_name":"Bottleneck","score":0.7985978722572327},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7183189392089844},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.6389576196670532},{"id":"https://openalex.org/keywords/pipeline-transport","display_name":"Pipeline transport","score":0.4759521186351776},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.43144404888153076},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4287988245487213},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.2126372754573822},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18389487266540527},{"id":"https://openalex.org/keywords/embedded-system","display_name":"Embedded system","score":0.14448294043540955},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12822067737579346},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.11500155925750732},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.10734686255455017}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.804803729057312},{"id":"https://openalex.org/C2780513914","wikidata":"https://www.wikidata.org/wiki/Q18210350","display_name":"Bottleneck","level":2,"score":0.7985978722572327},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7183189392089844},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.6389576196670532},{"id":"https://openalex.org/C175309249","wikidata":"https://www.wikidata.org/wiki/Q725864","display_name":"Pipeline transport","level":2,"score":0.4759521186351776},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.43144404888153076},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4287988245487213},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.2126372754573822},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18389487266540527},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.14448294043540955},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12822067737579346},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.11500155925750732},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.10734686255455017},{"id":"https://openalex.org/C87717796","wikidata":"https://www.wikidata.org/wiki/Q146326","display_name":"Environmental engineering","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm.2018.8621573","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2018.8621573","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","score":0.41999998688697815,"id":"https://metadata.un.org/sdg/9"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":28,"referenced_works":["https://openalex.org/W1596062789","https://openalex.org/W1919257374","https://openalex.org/W1981509058","https://openalex.org/W2048466306","https://openalex.org/W2049839797","https://openalex.org/W2093931624","https://openalex.org/W2095680943","https://openalex.org/W2108234281","https://openalex.org/W2108996658","https://openalex.org/W2131176533","https://openalex.org/W2131374955","https://openalex.org/W2147733682","https://openalex.org/W2152956782","https://openalex.org/W2170551349","https://openalex.org/W2177379918","https://openalex.org/W2189510244","https://openalex.org/W2283013536","https://openalex.org/W2574300709","https://openalex.org/W2590954301","https://openalex.org/W2597490071","https://openalex.org/W2604685034","https://openalex.org/W2903458665","https://openalex.org/W2951529834","https://openalex.org/W2953050047","https://openalex.org/W4394666350","https://openalex.org/W6635813232","https://openalex.org/W6674561012","https://openalex.org/W6687460725"],"related_works":["https://openalex.org/W4380433113","https://openalex.org/W4386072068","https://openalex.org/W252339960","https://openalex.org/W2390529043","https://openalex.org/W2378320433","https://openalex.org/W2358343511","https://openalex.org/W2051877971","https://openalex.org/W1970117064","https://openalex.org/W1787170397","https://openalex.org/W4292347844"],"abstract_inverted_index":{"In":[0,69],"recent":[1],"years,":[2],"the":[3,18,22,52,65],"amount":[4],"of":[5,21,30,67,118,122,154],"deoxyribonucleic":[6],"acid":[7],"(DNA)":[8],"sequencing":[9,32,45,59,158],"data":[10,33,60,87,100,152],"has":[11,34],"been":[12],"increasing":[13],"at":[14],"super-Moore's":[15],"rate":[16],"with":[17,128],"rapid":[19,81],"advance":[20],"Next":[23],"Generation":[24],"Sequencing":[25,150],"(NGS)":[26],"technology.":[27],"Globally,":[28],"processing":[29,61,83],"DNA":[31,58],"become":[35],"a":[36,80,114],"major":[37],"bottleneck":[38],"in":[39,120],"many":[40],"biomedical":[41],"research":[42],"labs":[43],"and":[44,47,90,124,142],"centers,":[46],"it":[48],"is":[49,95],"anticipated":[50],"that":[51],"associated":[53],"IT":[54],"costs":[55,66],"related":[56],"to":[57,71,78,97,130],"will":[62],"soon":[63],"exceed":[64],"sequencing.":[68],"response":[70],"this":[72],"challenge,":[73],"IMP":[74,94,119],"was":[75],"developed":[76],"recently":[77],"provide":[79],"secondary":[82,133],"pipeline":[84,141],"for":[85],"NGS":[86,99],"using":[88,146],"GPU":[89],"in-memory":[91],"computing":[92],"techniques.":[93],"able":[96],"process":[98],"100\u00d7":[101],"faster":[102],"than":[103],"existing":[104],"pipelines":[105],"without":[106],"compromising":[107],"variant":[108,125],"discovery":[109,126],"performance.":[110],"This":[111],"paper":[112],"presents":[113],"comprehensive":[115],"performance":[116,127],"evaluation":[117],"terms":[121],"speed":[123],"comparison":[129],"two":[131],"popular":[132],"analysis":[134],"pipelines,":[135],"namely,":[136],"GATK":[137],"best":[138],"practice":[139],"(BWA-GATK)":[140],"SpeedSeq":[143],"(BWA-FreeBayes)":[144],"pipeline,":[145],"nine":[147],"Whole":[148],"Genome":[149],"(WGS)":[151],"sets":[153],"NA12878":[155],"from":[156],"different":[157],"platforms.":[159]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2020,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}