{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,9]],"date-time":"2024-09-09T04:55:28Z","timestamp":1725857728058},"publisher-location":"Cham","reference-count":33,"publisher":"Springer International Publishing","isbn-type":[{"type":"print","value":"9783319413204"},{"type":"electronic","value":"9783319413211"}],"license":[{"start":{"date-parts":[[2016,1,1]],"date-time":"2016-01-01T00:00:00Z","timestamp":1451606400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016]]},"DOI":"10.1007\/978-3-319-41321-1_9","type":"book-chapter","created":{"date-parts":[[2016,6,14]],"date-time":"2016-06-14T06:19:15Z","timestamp":1465885155000},"page":"159-177","source":"Crossref","is-referenced-by-count":2,"title":["SPRITE: A Fast Parallel SNP Detection Pipeline"],"prefix":"10.1007","author":[{"given":"Vasudevan","family":"Rengasamy","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kamesh","family":"Madduri","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2016,6,15]]},"reference":[{"key":"9_CR1","doi-asserted-by":"crossref","DOI":"10.1007\/978-0-387-78909-5","volume-title":"The Burrows-Wheeler Transform: Data Compression, Suffix Arrays, and Pattern Matching","author":"D Adjeroh","year":"2008","unstructured":"Adjeroh, D., Bell, T.C., Mukherjee, A.: The Burrows-Wheeler Transform: Data Compression, Suffix Arrays, and Pattern Matching. Springer, Heidelberg (2008)"},{"key":"9_CR2","unstructured":"Burrows, M., Wheeler, D.J.: A block sorting lossless data compression algorithm. Technical report 124, Digital Equipment Corporation, Palo Alto, CA (1994)"},{"issue":"1","key":"9_CR3","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1186\/1471-2105-13-8","volume":"13","author":"D Challis","year":"2012","unstructured":"Challis, D., Yu, J., Evani, U.S., Jackson, A.R., Paithankar, S., Coarfa, C., Milosavljevic, A., Gibbs, R.A., Yu, F.: An integrative variant analysis suite for whole exome next-generation sequencing data. BMC Bioinformatics 13(1), 8 (2012)","journal-title":"BMC Bioinformatics"},{"key":"9_CR4","doi-asserted-by":"crossref","first-page":"966","DOI":"10.1038\/nmeth.3505","volume":"12","author":"C Chiang","year":"2015","unstructured":"Chiang, C., Layer, R.M., Faust, G.G., Lindberg, M.R., Rose, D.B., Garrison, E.P., Marth, G.T., Quinlan, A.R., Hall, I.M.: SpeedSeq: ultra-fast personal genome analysis and interpretation. Nat. Methods 12, 966\u2013968 (2015)","journal-title":"Nat. Methods"},{"key":"9_CR5","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1038\/ng.806","volume":"43","author":"M Depristo","year":"2011","unstructured":"Depristo, M., Banks, E., Poplin, R., Garimella, K., Maguire, J., Hartl, C.: A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43, 491\u20138 (2011)","journal-title":"Nat Genet"},{"key":"9_CR6","doi-asserted-by":"crossref","first-page":"2503","DOI":"10.1093\/bioinformatics\/btu314","volume":"30","author":"G Faust","year":"2014","unstructured":"Faust, G., Hall, I.: SAMBLASTER: fast duplicate marking and structural variant read extraction. Bioinformatics 30, 2503\u20135 (2014)","journal-title":"Bioinformatics"},{"key":"9_CR7","doi-asserted-by":"crossref","unstructured":"Ferragina, P., Manzini, G.: Opportunistic data structures with applications. In: Proceedings Symposium on Foundations of Computer Science, pp. 390\u2013398 (2000)","DOI":"10.1109\/SFCS.2000.892127"},{"key":"9_CR8","unstructured":"Garrison, E., Marth, G.: Haplotype-based variant detection from short-read sequencing (2012). http:\/\/arxiv.org\/abs\/1207.3907"},{"key":"9_CR9","unstructured":"GATK best practices. https:\/\/www.broadinstitute.org\/gatk\/guide\/best-practices.php . Accessed May 2016"},{"key":"9_CR10","unstructured":"Abecasis Lab GLF tools. http:\/\/www.sph.umich.edu\/csg\/abecasis\/glfTools . Accessed May 2016"},{"key":"9_CR11","doi-asserted-by":"crossref","unstructured":"Kathiresan, N., Temanni, M.R., Al-Ali, R.: Performance improvement of BWA MEM algorithm using data-parallel with concurrent parallelization. In: Proceedings of the International Conference on Parallel, Distributed and Grid Computing (PDGC) (2014)","DOI":"10.1109\/PDGC.2014.7030780"},{"issue":"1","key":"9_CR12","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1186\/s13059-014-0577-x","volume":"16","author":"B Kelly","year":"2015","unstructured":"Kelly, B., Fitch, J., Hu, Y., Corsmeier, D., Zhong, H., Wetzel, A., Nordquist, R., Newsom, D., White, P.: Churchill: an ultra-fast, deterministic, highly scalable and balanced parallelization strategy for the discovery of human genetic variation in clinical and population-scale genomics. Genome Biol. 16(1), 6 (2015)","journal-title":"Genome Biol."},{"issue":"4","key":"9_CR13","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","volume":"9","author":"B Langmead","year":"2012","unstructured":"Langmead, B., Salzberg, S.L.: Fast gapped-read alignment with Bowtie 2. Nat. Methods 9(4), 357\u2013359 (2012)","journal-title":"Nat. Methods"},{"issue":"21","key":"9_CR14","doi-asserted-by":"crossref","first-page":"2987","DOI":"10.1093\/bioinformatics\/btr509","volume":"27","author":"H Li","year":"2011","unstructured":"Li, H.: A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27(21), 2987\u20132993 (2011)","journal-title":"Bioinformatics"},{"key":"9_CR15","unstructured":"Li, H.: Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM (2013). http:\/\/arxiv.org\/abs\/1303.3997v2"},{"issue":"14","key":"9_CR16","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","volume":"25","author":"H Li","year":"2009","unstructured":"Li, H., Durbin, R.: Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25(14), 1754\u20131760 (2009)","journal-title":"Bioinformatics"},{"key":"9_CR17","doi-asserted-by":"crossref","unstructured":"Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R.: 1000 Genome Project Data Processing Subgroup: The aequence alignment\/map format and SAMtools. Bioinformatics 25(16), 2078\u20132079 (2009)","DOI":"10.1093\/bioinformatics\/btp352"},{"issue":"11","key":"9_CR18","doi-asserted-by":"crossref","first-page":"1851","DOI":"10.1101\/gr.078212.108","volume":"18","author":"H Li","year":"2008","unstructured":"Li, H., Ruan, J., Durbin, R.: Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 18(11), 1851\u20131858 (2008)","journal-title":"Genome Res."},{"issue":"15","key":"9_CR19","doi-asserted-by":"crossref","first-page":"1966","DOI":"10.1093\/bioinformatics\/btp336","volume":"25","author":"R Li","year":"2009","unstructured":"Li, R., Yu, C., Li, Y., Lam, T.-W., Yiu, S.-M., Kristiansen, K., Wang, J.: SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25(15), 1966\u20131967 (2009)","journal-title":"Bioinformatics"},{"issue":"6","key":"9_CR20","doi-asserted-by":"crossref","first-page":"878","DOI":"10.1093\/bioinformatics\/bts061","volume":"28","author":"C Liu","year":"2012","unstructured":"Liu, C., Wong, T., Wu, E., Luo, R., Yiu, S., Li, Y., Wang, B., Yu, C., Chu, X., Zhao, K., Li, R., Lam, T.: SOAP3: ultra-fast GPU-based parallel alignment tool for short reads. Bioinformatics 28(6), 878\u2013879 (2012)","journal-title":"Bioinformatics"},{"issue":"9","key":"9_CR21","doi-asserted-by":"crossref","first-page":"e75619","DOI":"10.1371\/journal.pone.0075619","volume":"8","author":"X Liu","year":"2013","unstructured":"Liu, X., Han, S., Wang, Z., Gelernter, J., Yang, B.-Z.: Variant callers for next-generation sequencing data: a comparison study. PLoS ONE 8(9), e75619 (2013)","journal-title":"PLoS ONE"},{"key":"9_CR22","doi-asserted-by":"crossref","first-page":"e421","DOI":"10.7717\/peerj.421","volume":"2","author":"R Luo","year":"2014","unstructured":"Luo, R., Wong, Y.-L., Law, W.-C., Lee, L.-K., Cheung, J., Liu, C.-M., Lam, T.-W.: BALSA: integrated secondary analysis for whole-genome and whole-exome sequencing, accelerated by GPU. PeerJ 2, e421 (2014)","journal-title":"PeerJ"},{"key":"9_CR23","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1038\/nrg2986","volume":"12","author":"R Nielsen","year":"2011","unstructured":"Nielsen, R., Paul, J., Albrechtsen, A., Song, Y.: Genotype and SNP calling from next-generation sequencing data. Nat. Rev. Genet. 12, 443\u2013451 (2011)","journal-title":"Nat. Rev. Genet."},{"issue":"1","key":"9_CR24","first-page":"1","volume":"1","author":"D Peters","year":"2012","unstructured":"Peters, D., Luo, X., Qiu, K., Liang, P.: Speeding up large-scale next generation sequencing data analysis with pBWA. J. Appl. Bioinform. Comput. Biol. 1(1), 1\u20136 (2012)","journal-title":"J. Appl. Bioinform. Comput. Biol."},{"key":"9_CR25","unstructured":"Picard tools. http:\/\/broadinstitute.github.io\/picard . Accessed Dec 2015"},{"key":"9_CR26","unstructured":"pMap: Parallel sequence mapping tool. http:\/\/bmi.osu.edu\/hpc\/software\/pmap\/pmap.html . Accessed May 2016"},{"issue":"16","key":"9_CR27","doi-asserted-by":"crossref","first-page":"2041","DOI":"10.1093\/bioinformatics\/btt314","volume":"29","author":"C Raczy","year":"2013","unstructured":"Raczy, C., Petrovski, R., Saunders, C.T., Chorny, I., Kruglyak, S., Margulies, E.H., Chuang, H.-Y., Kllberg, M., Kumar, S.A., Liao, A., Little, K.M., Str\u00f6mberg, M.P., Tanner, S.W.: Isaac: ultra-fast whole-genome secondary analysis on Illumina sequencing platforms. Bioinformatics 29(16), 2041\u20132043 (2013)","journal-title":"Bioinformatics"},{"key":"9_CR28","unstructured":"Rengasamy, V., Madduri, K.: Engineering a high-performance SNP detection pipeline. Technical report, The Pennsylvania State University (2015)"},{"issue":"5","key":"9_CR29","doi-asserted-by":"crossref","first-page":"e1000386","DOI":"10.1371\/journal.pcbi.1000386","volume":"5","author":"SM Rumble","year":"2009","unstructured":"Rumble, S.M., Lacroute, P., Dalca, A.V., Fiume, M., Sidow, A., Brudno, M.: Shrimp: accurate mapping of short color-space reads. PLoS Comput. Biol. 5(5), e1000386 (2009)","journal-title":"PLoS Comput. Biol."},{"key":"9_CR30","unstructured":"Sambamba: process your BAM data faster! http:\/\/lomereiter.github.io\/sambamba\/ . Accessed May 2016"},{"key":"9_CR31","unstructured":"Single Nucleotide Polymorphism - SNPedia. http:\/\/www.snpedia.com\/index.php\/Single_Nucleotide_Polymorphism . Accessed May 2016"},{"issue":"19","key":"9_CR32","doi-asserted-by":"crossref","first-page":"2787","DOI":"10.1093\/bioinformatics\/btu345","volume":"30","author":"A Talwalkar","year":"2014","unstructured":"Talwalkar, A., Liptrap, J., Newcomb, J., Hartl, C., Terhorst, J., Curtis, K., Bresler, M., Song, Y.S., Jordan, M.I., Patterson, D.: SMaSH: a benchmarking toolkit for human genome variant calling. Bioinformatics 30(19), 2787\u20132795 (2014)","journal-title":"Bioinformatics"},{"key":"9_CR33","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1038\/nbt.2835","volume":"32","author":"J Zook","year":"2014","unstructured":"Zook, J., Chapman, B., Wang, J., Mittelman, D., Hofmann, O., Hide, W.: Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls. Nat. Biotechnol. 32, 246\u2013251 (2014)","journal-title":"Nat. Biotechnol."}],"container-title":["Lecture Notes in Computer Science","High Performance Computing"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-319-41321-1_9","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2017,6,24]],"date-time":"2017-06-24T12:20:38Z","timestamp":1498306838000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-319-41321-1_9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016]]},"ISBN":["9783319413204","9783319413211"],"references-count":33,"URL":"https:\/\/doi.org\/10.1007\/978-3-319-41321-1_9","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2016]]}}}