{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T03:48:12Z","timestamp":1772164092280,"version":"3.50.1"},"publisher-location":"New York, NY, USA","reference-count":28,"publisher":"ACM","license":[{"start":{"date-parts":[[2018,2,10]],"date-time":"2018-02-10T00:00:00Z","timestamp":1518220800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.acm.org\/publications\/policies\/copyright_policy#Background"}],"funder":[{"name":"The National Key Research and Development Program of China","award":["2016YFB0201305,2016YFB0200504,2016YFB0200803,2016YFB0200300"],"award-info":[{"award-number":["2016YFB0201305,2016YFB0200504,2016YFB0200803,2016YFB0200300"]}]},{"name":"National Natural Science Foundation of China","award":["61521092,91430218,31327901,61472395,61432018"],"award-info":[{"award-number":["61521092,91430218,31327901,61472395,61432018"]}]}],"content-domain":{"domain":["dl.acm.org"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2018,2,10]]},"DOI":"10.1145\/3178487.3178511","type":"proceedings-article","created":{"date-parts":[[2018,2,6]],"date-time":"2018-02-06T13:12:23Z","timestamp":1517922743000},"page":"317-328","update-policy":"https:\/\/doi.org\/10.1145\/crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["High-performance genomic analysis framework with in-memory computing"],"prefix":"10.1145","author":[{"given":"Xueqi","family":"Li","sequence":"first","affiliation":[{"name":"Institute of Computing Technology, Chinese Academy of Sciences"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guangming","family":"Tan","sequence":"additional","affiliation":[{"name":"Institute of Computing Technology, Chinese Academy of Sciences"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bingchen","family":"Wang","sequence":"additional","affiliation":[{"name":"University of Chinese Academy of Sciences"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ninghui","family":"Sun","sequence":"additional","affiliation":[{"name":"University of Chinese Academy of Sciences"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"320","published-online":{"date-parts":[[2018,2,10]]},"reference":[{"key":"e_1_3_2_1_1_1","unstructured":"2016. HG19 Human Genome Download. http:\/\/hgdownload.cse.ucsc.edu\/goldenPath\/hg19\/bigZips\/. (2016).  2016. HG19 Human Genome Download. http:\/\/hgdownload.cse.ucsc.edu\/goldenPath\/hg19\/bigZips\/. (2016)."},{"key":"e_1_3_2_1_2_1","unstructured":"2016. Picard: A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM\/BAM\/CRAM and VCF. http:\/\/broadinstitute.github.io\/picard\/. (2016).  2016. Picard: A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM\/BAM\/CRAM and VCF. http:\/\/broadinstitute.github.io\/picard\/. (2016)."},{"key":"e_1_3_2_1_3_1","volume-title":"Persona: A High-Performance Bioinformatics Framework. In USENIX Annual Technical Conference","author":"Byma Stuart Anthony","year":"2017","unstructured":"Stuart Anthony Byma , Sam David Whitlock , Laura Flueratoru , Ethan Tseng , Christos Kozyrakis , Edouard Bugnion , and James Larus . 2017 . Persona: A High-Performance Bioinformatics Framework. In USENIX Annual Technical Conference 2017. Stuart Anthony Byma, Sam David Whitlock, Laura Flueratoru, Ethan Tseng, Christos Kozyrakis, Edouard Bugnion, and James Larus. 2017. Persona: A High-Performance Bioinformatics Framework. In USENIX Annual Technical Conference 2017."},{"key":"e_1_3_2_1_4_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr014"},{"key":"e_1_3_2_1_5_1","unstructured":"Apache Software Foundation. Online. Apache Hadoop. http:\/\/hadoop.apache.org\/. (Online).  Apache Software Foundation. Online. Apache Hadoop. http:\/\/hadoop.apache.org\/. (Online)."},{"key":"e_1_3_2_1_6_1","volume-title":"Human genome sequencing in health and disease. Annual review of medicine 63","author":"Gonzaga-Jauregui Claudia","year":"2012","unstructured":"Claudia Gonzaga-Jauregui , James R Lupski , and Richard A Gibbs . 2012. Human genome sequencing in health and disease. Annual review of medicine 63 ( 2012 ), 35--61. Claudia Gonzaga-Jauregui, James R Lupski, and Richard A Gibbs. 2012. Human genome sequencing in health and disease. Annual review of medicine 63 (2012), 35--61."},{"key":"e_1_3_2_1_7_1","unstructured":"Illumina. 2012. HiSeq Sequencing System. http:\/\/www.illumina.com\/. (2012).  Illumina. 2012. HiSeq Sequencing System. http:\/\/www.illumina.com\/. (2012)."},{"key":"e_1_3_2_1_8_1","unstructured":"illumina. 2017. NovaSeq. https:\/\/www.illumina.com\/systems\/sequencing-platforms\/novaseq.html. (2017).  illumina. 2017. NovaSeq. https:\/\/www.illumina.com\/systems\/sequencing-platforms\/novaseq.html. (2017)."},{"key":"e_1_3_2_1_9_1","unstructured":"Broad Institute. Online. GATK-4. https:\/\/github.com\/broadinstitute\/gatk. (Online).  Broad Institute. Online. GATK-4. https:\/\/github.com\/broadinstitute\/gatk. (Online)."},{"key":"e_1_3_2_1_10_1","unstructured":"Broad Institute. Online. GATK Queue. http:\/\/gatkforums.broadinstitute.org\/discussion\/1306\/overview-of-queue. (Online).  Broad Institute. Online. GATK Queue. http:\/\/gatkforums.broadinstitute.org\/discussion\/1306\/overview-of-queue. (Online)."},{"key":"e_1_3_2_1_11_1","volume-title":"On the future of genomic data. science 331, 6018","author":"Kahn Scott D","year":"2011","unstructured":"Scott D Kahn . 2011. On the future of genomic data. science 331, 6018 ( 2011 ), 728--729. Scott D Kahn. 2011. On the future of genomic data. science 331, 6018 (2011), 728--729."},{"key":"e_1_3_2_1_12_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-014-0577-x"},{"key":"e_1_3_2_1_13_1","doi-asserted-by":"publisher","DOI":"10.1145\/2807591.2807595"},{"key":"e_1_3_2_1_14_1","volume-title":"Detecting and annotating genetic variations using the HugeSeq pipeline. Nat Biotech 30, 3 (03","author":"Lam Hugo Y K","year":"2012","unstructured":"Hugo Y K Lam , Cuiping Pan , Michael J Clark , Phil Lacroute , Rui Chen , Rajini Haraksingh , Maeve O'Huallachain , Mark B Gerstein , Jeffrey M Kidd , Carlos D Bustamante , and Michael Snyder . 2012. Detecting and annotating genetic variations using the HugeSeq pipeline. Nat Biotech 30, 3 (03 2012 ), 226--229. Hugo Y K Lam, Cuiping Pan, Michael J Clark, Phil Lacroute, Rui Chen, Rajini Haraksingh, Maeve O'Huallachain, Mark B Gerstein, Jeffrey M Kidd, Carlos D Bustamante, and Michael Snyder. 2012. Detecting and annotating genetic variations using the HugeSeq pipeline. Nat Biotech 30, 3 (03 2012), 226--229."},{"key":"e_1_3_2_1_15_1","doi-asserted-by":"crossref","unstructured":"Ben Langmead Cole Trapnell Mihai Pop Steven L Salzberg etal 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome biol 10 3 (2009) R25.  Ben Langmead Cole Trapnell Mihai Pop Steven L Salzberg et al. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome biol 10 3 (2009) R25.","DOI":"10.1186\/gb-2009-10-3-r25"},{"key":"e_1_3_2_1_16_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp324"},{"key":"e_1_3_2_1_17_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp352"},{"key":"e_1_3_2_1_18_1","volume-title":"Bioinformatics and Biomedicine (BIBM), 2016 IEEE International Conference on. IEEE, 747--751","author":"Li Xueqi","year":"2016","unstructured":"Xueqi Li , Guangming Tan , Chunming Zhang , Xu Li , Zhonghai Zhang , and Ninghui Sun . 2016 . Accelerating large-scale genomic analysis with Spark . In Bioinformatics and Biomedicine (BIBM), 2016 IEEE International Conference on. IEEE, 747--751 . Xueqi Li, Guangming Tan, Chunming Zhang, Xu Li, Zhonghai Zhang, and Ninghui Sun. 2016. Accelerating large-scale genomic analysis with Spark. In Bioinformatics and Biomedicine (BIBM), 2016 IEEE International Conference on. IEEE, 747--751."},{"key":"e_1_3_2_1_19_1","volume-title":"Adam: Genomics formats and processing patterns for cloud scale computing","author":"Massie Matt","year":"2013","unstructured":"Matt Massie , Frank Nothaft , Christopher Hartl , Christos Kozanitis , Andr\u00e9 Schumacher , Anthony D Joseph , and David A Patterson . 2013 . Adam: Genomics formats and processing patterns for cloud scale computing . University of California , Berkeley Technical Report, No. UCB\/EECS-2013 207 (2013). Matt Massie, Frank Nothaft, Christopher Hartl, Christos Kozanitis, Andr\u00e9 Schumacher, Anthony D Joseph, and David A Patterson. 2013. Adam: Genomics formats and processing patterns for cloud scale computing. University of California, Berkeley Technical Report, No. UCB\/EECS-2013 207 (2013)."},{"key":"e_1_3_2_1_20_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.107524.110"},{"key":"e_1_3_2_1_21_1","volume-title":"Sequencing technologies-the next generation. Nature reviews genetics 11, 1","author":"Metzker Michael L","year":"2010","unstructured":"Michael L Metzker . 2010. Sequencing technologies-the next generation. Nature reviews genetics 11, 1 ( 2010 ), 31--46. Michael L Metzker. 2010. Sequencing technologies-the next generation. Nature reviews genetics 11, 1 (2010), 31--46."},{"key":"e_1_3_2_1_22_1","volume-title":"Proceedings of the 5th International Conference on Bioinformatics and Computational Biology (BICoB)","author":"Mohamed Nabeel M","year":"2013","unstructured":"Nabeel M Mohamed , Heshan Lin , and Wuchun Feng . 2013 . Accelerating data-intensive genome analysis in the cloud . In Proceedings of the 5th International Conference on Bioinformatics and Computational Biology (BICoB) , Honolulu, Hawaii, USA. Nabeel M Mohamed, Heshan Lin, and Wuchun Feng. 2013. Accelerating data-intensive genome analysis in the cloud. In Proceedings of the 5th International Conference on Bioinformatics and Computational Biology (BICoB), Honolulu, Hawaii, USA."},{"key":"e_1_3_2_1_23_1","doi-asserted-by":"publisher","DOI":"10.1145\/2723372.2742787"},{"key":"e_1_3_2_1_24_1","first-page":"293","article-title":"Making Sense of Performance in Data Analytics Frameworks","volume":"15","author":"Ousterhout Kay","year":"2015","unstructured":"Kay Ousterhout , Ryan Rasti , Sylvia Ratnasamy , Scott Shenker , Byung-Gon Chun , and V ICSI. 2015 . Making Sense of Performance in Data Analytics Frameworks .. In NSDI , Vol. 15. 293 -- 307 . Kay Ousterhout, Ryan Rasti, Sylvia Ratnasamy, Scott Shenker, Byung-Gon Chun, and V ICSI. 2015. Making Sense of Performance in Data Analytics Frameworks.. In NSDI, Vol. 15. 293--307.","journal-title":"NSDI"},{"key":"e_1_3_2_1_25_1","volume-title":"Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature protocols 7, 3","author":"Trapnell Cole","year":"2012","unstructured":"Cole Trapnell , Adam Roberts , Loyal Goff , Geo Pertea , Daehwan Kim , David R Kelley , Harold Pimentel , Steven L Salzberg , John L Rinn , and Lior Pachter . 2012. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature protocols 7, 3 ( 2012 ), 562. Cole Trapnell, Adam Roberts, Loyal Goff, Geo Pertea, Daehwan Kim, David R Kelley, Harold Pimentel, Steven L Salzberg, John L Rinn, and Lior Pachter. 2012. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature protocols 7, 3 (2012), 562."},{"key":"e_1_3_2_1_26_1","volume-title":"Faster and More Accurate Sequence Alignment with SNAP. CoRR abs\/1111.5572","author":"Zaharia Matei","year":"2011","unstructured":"Matei Zaharia , William J. Bolosky , Kristal Curtis , Armando Fox , David A. Patterson , Scott Shenker , Ion Stoica , Richard M. Karp , and Taylor Sittler . 2011. Faster and More Accurate Sequence Alignment with SNAP. CoRR abs\/1111.5572 ( 2011 ). arXiv:1111.5572 http:\/\/arxiv.org\/abs\/1111.5572 Matei Zaharia, William J. Bolosky, Kristal Curtis, Armando Fox, David A. Patterson, Scott Shenker, Ion Stoica, Richard M. Karp, and Taylor Sittler. 2011. Faster and More Accurate Sequence Alignment with SNAP. CoRR abs\/1111.5572 (2011). arXiv:1111.5572 http:\/\/arxiv.org\/abs\/1111.5572"},{"key":"e_1_3_2_1_27_1","volume-title":"Proceedings of the 9th USENIX Conference on Networked Systems Design and Implementation (NSDI'12)","author":"Zaharia Matei","year":"2012","unstructured":"Matei Zaharia , Mosharaf Chowdhury , Tathagata Das , Ankur Dave , Justin Ma , Murphy McCauley , Michael J. Franklin , Scott Shenker , and Ion Stoica . 2012 . Resilient Distributed Datasets: A Fault-tolerant Abstraction for In-memory Cluster Computing . In Proceedings of the 9th USENIX Conference on Networked Systems Design and Implementation (NSDI'12) . USENIX Association, Berkeley, CA, USA, 2--2. http:\/\/dl.acm.org\/citation.cfm?id=2228298.2228301 Matei Zaharia, Mosharaf Chowdhury, Tathagata Das, Ankur Dave, Justin Ma, Murphy McCauley, Michael J. Franklin, Scott Shenker, and Ion Stoica. 2012. Resilient Distributed Datasets: A Fault-tolerant Abstraction for In-memory Cluster Computing. In Proceedings of the 9th USENIX Conference on Networked Systems Design and Implementation (NSDI'12). USENIX Association, Berkeley, CA, USA, 2--2. http:\/\/dl.acm.org\/citation.cfm?id=2228298.2228301"},{"key":"e_1_3_2_1_28_1","volume-title":"Optimizing Burrows-Wheeler Transform-Based Sequence Alignment on Multicore Architectures. CCGRID","author":"Zhang Jing","year":"2013","unstructured":"Jing Zhang , Heshan Lin , Pavan Balaji , and Wu-chun Feng. 2013. Optimizing Burrows-Wheeler Transform-Based Sequence Alignment on Multicore Architectures. CCGRID ( 2013 ), 377--384. Jing Zhang, Heshan Lin, Pavan Balaji, and Wu-chun Feng. 2013. Optimizing Burrows-Wheeler Transform-Based Sequence Alignment on Multicore Architectures. CCGRID (2013), 377--384."}],"event":{"name":"PPoPP '18: 23nd ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","location":"Vienna Austria","acronym":"PPoPP '18","sponsor":["SIGPLAN ACM Special Interest Group on Programming Languages","SIGHPC ACM Special Interest Group on High Performance Computing, Special Interest Group on High Performance Computing"]},"container-title":["Proceedings of the 23rd ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming"],"original-title":[],"link":[{"URL":"https:\/\/dl.acm.org\/doi\/10.1145\/3178487.3178511","content-type":"unspecified","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/dl.acm.org\/doi\/pdf\/10.1145\/3178487.3178511","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,17]],"date-time":"2025-06-17T21:39:08Z","timestamp":1750196348000},"score":1,"resource":{"primary":{"URL":"https:\/\/dl.acm.org\/doi\/10.1145\/3178487.3178511"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,2,10]]},"references-count":28,"alternative-id":["10.1145\/3178487.3178511","10.1145\/3178487"],"URL":"https:\/\/doi.org\/10.1145\/3178487.3178511","relation":{"is-identical-to":[{"id-type":"doi","id":"10.1145\/3200691.3178511","asserted-by":"object"}]},"subject":[],"published":{"date-parts":[[2018,2,10]]},"assertion":[{"value":"2018-02-10","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}