{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,9]],"date-time":"2024-09-09T14:14:08Z","timestamp":1725891248711},"publisher-location":"Berlin, Heidelberg","reference-count":18,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"type":"print","value":"9783642314995"},{"type":"electronic","value":"9783642315008"}],"license":[{"start":{"date-parts":[[2012,1,1]],"date-time":"2012-01-01T00:00:00Z","timestamp":1325376000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012]]},"DOI":"10.1007\/978-3-642-31500-8_28","type":"book-chapter","created":{"date-parts":[[2012,7,3]],"date-time":"2012-07-03T15:09:08Z","timestamp":1341328148000},"page":"272-280","source":"Crossref","is-referenced-by-count":0,"title":["Parallel and Memory-Efficient Reads Indexing for Genome Assembly"],"prefix":"10.1007","author":[{"given":"Guillaume","family":"Chapuis","sequence":"first","affiliation":[]},{"given":"Rayan","family":"Chikhi","sequence":"additional","affiliation":[]},{"given":"Dominique","family":"Lavenier","sequence":"additional","affiliation":[]}],"member":"297","reference":[{"key":"28_CR1","doi-asserted-by":"crossref","unstructured":"Ariyaratne, P.N., Sung, W.: PE-Assembler: de novo assembler using short paired-end reads. Bioinformatics (December 2010)","DOI":"10.1093\/bioinformatics\/btq626"},{"key":"28_CR2","doi-asserted-by":"crossref","unstructured":"Boisvert, S., Laviolette, F., Corbeil, J.: Ray: Simultaneous assembly of reads from a mix of High-Throughput sequencing technologies. Journal of Computational Biology, 3389\u20133402 (2010)","DOI":"10.1089\/cmb.2009.0238"},{"issue":"8","key":"28_CR3","doi-asserted-by":"publisher","first-page":"23501","DOI":"10.1371\/journal.pone.0023501","volume":"6","author":"J.A. Chapman","year":"2011","unstructured":"Chapman, J.A., Ho, I., Sunkara, S., Luo, S., Schroth, G.P., Rokhsar, D.S.: Meraculous: De novo genome assembly with short Paired-End reads. PloS One\u00a06(8), e23501 (2011)","journal-title":"PloS One"},{"key":"28_CR4","doi-asserted-by":"crossref","unstructured":"Chikhi, R., Lavenier, D.: Localized genome assembly from reads to scaffolds: practical traversal of the paired string graph. Algorithms in Bioinformatics, 39\u201348 (2011)","DOI":"10.1007\/978-3-642-23038-7_4"},{"key":"28_CR5","doi-asserted-by":"crossref","unstructured":"Conway, T.C., Bromage, A.J.: Succinct data structures for assembling large genomes. Bioinformatics (2011)","DOI":"10.1093\/bioinformatics\/btq697"},{"issue":"4","key":"28_CR6","doi-asserted-by":"publisher","first-page":"552","DOI":"10.1145\/1082036.1082039","volume":"52","author":"P. Ferragina","year":"2005","unstructured":"Ferragina, P., Manzini, G.: Indexing compressed text. Journal of the ACM (JACM)\u00a052(4), 552\u2013581 (2005)","journal-title":"Journal of the ACM (JACM)"},{"issue":"suppl. 1","key":"28_CR7","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1186\/1471-2105-10-S1-S14","volume":"10","author":"B. Jackson","year":"2009","unstructured":"Jackson, B., Schnable, P., Aluru, S.: Parallel short sequence assembly of transcriptomes. BMC Bioinformatics\u00a010(suppl. 1), S14 (2009)","journal-title":"BMC Bioinformatics"},{"issue":"1","key":"28_CR8","doi-asserted-by":"publisher","first-page":"560","DOI":"10.1186\/1471-2105-11-560","volume":"11","author":"V. Kundeti","year":"2010","unstructured":"Kundeti, V., Rajasekaran, S., Dinh, H., Vaughn, M., Thapar, V.: Efficient parallel and out of core algorithms for constructing large bi-directed de bruijn graphs. BMC Bioinformatics\u00a011(1), 560 (2010)","journal-title":"BMC Bioinformatics"},{"issue":"2","key":"28_CR9","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1101\/gr.097261.109","volume":"20","author":"R. Li","year":"2010","unstructured":"Li, R., Zhu, H., Ruan, J., Qian, W., Fang, X., Shi, Z., Li, Y., Li, S., Shan, G., Kristiansen, K., Li, S., Yang, H., Wang, J., Wang, J.: De novo assembly of human genomes with massively parallel short read sequencing. Genome Research\u00a020(2), 265\u2013272 (2010), \n                    \n                      http:\/\/genome.cshlp.org\/content\/20\/2\/265.abstract","journal-title":"Genome Research"},{"key":"28_CR10","doi-asserted-by":"crossref","unstructured":"Miller, J.R., Koren, S., Sutton, G.: Assembly algorithms for next-generation sequencing data. Genomics (2010)","DOI":"10.1016\/j.ygeno.2010.03.001"},{"key":"28_CR11","doi-asserted-by":"crossref","unstructured":"Okanohara, D., Sadakane, K.: Practical entropy-compressed rank\/select dictionary. Arxiv preprint cs\/0610001 (2006)","DOI":"10.1137\/1.9781611972870.6"},{"key":"28_CR12","series-title":"LNCS","doi-asserted-by":"publisher","first-page":"426","DOI":"10.1007\/978-3-642-12683-3_28","volume-title":"Research in Computational Molecular Biology","author":"Y. Peng","year":"2010","unstructured":"Peng, Y., Leung, H.C.M., Yiu, S.M., Chin, F.Y.L.: IDBA \u2013 A Practical Iterative de Bruijn Graph De Novo Assembler. In: Berger, B. (ed.) RECOMB 2010. LNCS, vol.\u00a06044, pp. 426\u2013440. Springer, Heidelberg (2010)"},{"issue":"4","key":"28_CR13","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1145\/1290672.1290680","volume":"3","author":"R. Raman","year":"2007","unstructured":"Raman, R., Raman, V., Satti, S.R.: Succinct indexable dictionaries with applications to encoding k-ary trees, prefix sums and multisets. ACM Transactions on Algorithms (TALG)\u00a03(4), 43\u2013es (2007)","journal-title":"ACM Transactions on Algorithms (TALG)"},{"issue":"10","key":"28_CR14","doi-asserted-by":"publisher","first-page":"103","DOI":"10.1186\/gb-2009-10-10-r103","volume":"10","author":"T. Shea","year":"2009","unstructured":"Shea, T., Williams, L., Young, S., Nusbaum, C., Jaffe, D., MacCallum, I., Przybylski, D., Gnerre, S., Burton, J., Shlyakhter, I., Gnirke, A., Malek, J., McKernan, K., Ranade, S.: ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads. Genome Biology\u00a010(10), R103 (2009), \n                    \n                      http:\/\/genomebiology.com\/2009\/10\/10\/R103","journal-title":"Genome Biology"},{"issue":"12","key":"28_CR15","doi-asserted-by":"publisher","first-page":"367","DOI":"10.1093\/bioinformatics\/btq217","volume":"26","author":"J.T. Simpson","year":"2010","unstructured":"Simpson, J.T., Durbin, R.: Efficient construction of an assembly string graph using the FM-index. Bioinformatics\u00a026(12), i367 (2010)","journal-title":"Bioinformatics"},{"issue":"6","key":"28_CR16","doi-asserted-by":"publisher","first-page":"1117","DOI":"10.1101\/gr.089532.108","volume":"19","author":"J.T. Simpson","year":"2009","unstructured":"Simpson, J.T., Wong, K., Jackman, S.D., Schein, J.E., Jones, S.J., Birol, I.: ABySS: a parallel assembler for short read sequence data. Genome Research\u00a019(6), 1117\u20131123 (2009)","journal-title":"Genome Research"},{"issue":"4","key":"28_CR17","doi-asserted-by":"publisher","first-page":"500","DOI":"10.1093\/bioinformatics\/btl629","volume":"23","author":"R.L. Warren","year":"2007","unstructured":"Warren, R.L., Sutton, G.G., Jones, S.J.M., Holt, R.A.: Assembling millions of short DNA sequences using SSAKE. Bioinformatics\u00a023(4), 500\u2013501 (2007), \n                    \n                      http:\/\/bioinformatics.oxfordjournals.org\/cgi\/content\/abstract\/23\/4\/500","journal-title":"Bioinformatics"},{"issue":"5","key":"28_CR18","doi-asserted-by":"publisher","first-page":"821","DOI":"10.1101\/gr.074492.107","volume":"18","author":"D.R. Zerbino","year":"2008","unstructured":"Zerbino, D.R., Birney, E.: Velvet: Algorithms for de novo short read assembly using de bruijn graphs. Genome Research\u00a018(5), 821\u2013829 (2008), \n                    \n                      http:\/\/genome.cshlp.org\/content\/18\/5\/821.abstract","journal-title":"Genome Research"}],"container-title":["Lecture Notes in Computer Science","Parallel Processing and Applied Mathematics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-642-31500-8_28","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,5,20]],"date-time":"2019-05-20T00:50:53Z","timestamp":1558313453000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-642-31500-8_28"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012]]},"ISBN":["9783642314995","9783642315008"],"references-count":18,"URL":"https:\/\/doi.org\/10.1007\/978-3-642-31500-8_28","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2012]]}}}