{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,9]],"date-time":"2024-09-09T18:09:04Z","timestamp":1725905344867},"publisher-location":"Cham","reference-count":21,"publisher":"Springer International Publishing","isbn-type":[{"type":"print","value":"9783319633114"},{"type":"electronic","value":"9783319633121"}],"license":[{"start":{"date-parts":[[2017,1,1]],"date-time":"2017-01-01T00:00:00Z","timestamp":1483228800000},"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":[[2017]]},"DOI":"10.1007\/978-3-319-63312-1_38","type":"book-chapter","created":{"date-parts":[[2017,7,19]],"date-time":"2017-07-19T15:43:13Z","timestamp":1500478993000},"page":"428-438","source":"Crossref","is-referenced-by-count":1,"title":["LSLS: A Novel Scaffolding Method Based on Path Extension"],"prefix":"10.1007","author":[{"given":"Min","family":"Li","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Li","family":"Tang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhongxiang","family":"Liao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Junwei","family":"Luo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fangxiang","family":"Wu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yi","family":"Pan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jianxin","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2017,7,20]]},"reference":[{"issue":"4","key":"38_CR1","doi-asserted-by":"crossref","first-page":"641","DOI":"10.1373\/clinchem.2008.112789","volume":"55","author":"KV Voelkerding","year":"2009","unstructured":"Voelkerding, K.V., Dames, S.A., Durtschi, J.D.: Next-generation sequencing: from basic research to diagnostics. Clin. Chem. 55(4), 641\u2013658 (2009)","journal-title":"Clin. Chem."},{"issue":"6","key":"38_CR2","doi-asserted-by":"crossref","first-page":"825","DOI":"10.1093\/bioinformatics\/btu762","volume":"31","author":"J Luo","year":"2015","unstructured":"Luo, J., Wang, J., Zhang, Z., Wu, F.X., Li, M., Pan, Y.: Epga: de novo assembly using the distributions of reads and insert size. Bioinformatics 31(6), 825\u2013833 (2015)","journal-title":"Bioinformatics"},{"issue":"11","key":"38_CR3","doi-asserted-by":"crossref","first-page":"1429","DOI":"10.1093\/bioinformatics\/bts175","volume":"28","author":"AA Gritsenko","year":"2012","unstructured":"Gritsenko, A.A., Nijkamp, J.F., Reinders, M.J.T., Ridder, D.D.: Grass: a generic algorithm for scaffolding next-generation sequencing assemblies. Bioinformatics 28(11), 1429 (2012)","journal-title":"Bioinformatics"},{"issue":"23","key":"38_CR4","doi-asserted-by":"crossref","first-page":"3259","DOI":"10.1093\/bioinformatics\/btr562","volume":"27","author":"L Salmela","year":"2011","unstructured":"Salmela, L., M\u00e4kinen, V., V\u00e4lim\u00e4ki, N., Ylinen, J., Ukkonen, E.: Fast scaffolding with small independent mixed integer programs. Bioinformatics 27(23), 3259\u20133265 (2011)","journal-title":"Bioinformatics"},{"issue":"1","key":"38_CR5","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1186\/1471-2105-11-345","volume":"11","author":"A Dayarian","year":"2010","unstructured":"Dayarian, A., Michael, T.P., Sengupta, A.M.: Sopra: scaffolding algorithm for paired reads via statistical optimization. BMC Bioinform. 11(1), 345 (2010)","journal-title":"BMC Bioinform."},{"issue":"21","key":"38_CR6","doi-asserted-by":"crossref","first-page":"2964","DOI":"10.1093\/bioinformatics\/btr520","volume":"27","author":"S Koren","year":"2011","unstructured":"Koren, S., Treangen, T.J., Pop, M.: Bambus 2: scaffolding metagenomes. Bioinformatics 27(21), 2964\u20132971 (2011)","journal-title":"Bioinformatics"},{"issue":"4","key":"38_CR7","doi-asserted-by":"crossref","first-page":"428","DOI":"10.1093\/bioinformatics\/bts716","volume":"29","author":"N Donmez","year":"2013","unstructured":"Donmez, N., Brudno, M.: Scarpa: scaffolding reads with practical algorithms. Bioinformatics 29(4), 428 (2013)","journal-title":"Bioinformatics"},{"issue":"11","key":"38_CR8","doi-asserted-by":"crossref","first-page":"1681","DOI":"10.1089\/cmb.2011.0170","volume":"18","author":"S Gao","year":"2011","unstructured":"Gao, S., Nagarajan, N., Sung, W.K.: Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences. J. Comput. Biol. J. Comput. Mol. Cell Biol. 18(11), 1681\u20131691 (2011)","journal-title":"J. Comput. Biol. J. Comput. Mol. Cell Biol."},{"issue":"3","key":"38_CR9","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1101\/gr.126953.111","volume":"22","author":"JT Simpson","year":"2012","unstructured":"Simpson, J.T., Durbin, R.: Efficient de novo assembly of large genomes using compressed data structures. Genome Res. 22(3), 549\u2013556 (2012)","journal-title":"Genome Res."},{"issue":"6","key":"38_CR10","doi-asserted-by":"crossref","first-page":"1117","DOI":"10.1101\/gr.089532.108","volume":"19","author":"JT Simpson","year":"2009","unstructured":"Simpson, J.T., Wong, K., Jackman, S.D., et al.: Abyss: a parallel assembler for short read sequence data. Genome Res. 19(6), 1117 (2009)","journal-title":"Genome Res."},{"key":"38_CR11","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"222","DOI":"10.1007\/978-3-319-16706-0_22","volume-title":"Research in Computational Molecular Biology","author":"I Mandric","year":"2015","unstructured":"Mandric, I., Zelikovsky, A.: ScaffMatch: scaffolding algorithm based on maximum weight matching. In: Przytycka, Teresa M. (ed.) RECOMB 2015. LNCS, vol. 9029, pp. 222\u2013223. Springer, Cham (2015). doi:\n10.1007\/978-3-319-16706-0_22"},{"key":"38_CR12","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1093\/bioinformatics\/btw597","volume":"33","author":"J Luo","year":"2016","unstructured":"Luo, J., Wang, J., Zhen, Z., Min, L., Wu, F.X.: Boss: a novel scaffolding algorithm based on an optimized scaffold graph. Bioinformatics 33, 169\u2013176 (2016). btw597","journal-title":"Bioinformatics"},{"issue":"2","key":"38_CR13","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1093\/bioinformatics\/btq626","volume":"27","author":"PN Ariyaratne","year":"2011","unstructured":"Ariyaratne, P.N., Sung, W.K.: Pe-assembler: de novo assembler using short paired-end reads. Bioinformatics 27(2), 167 (2011)","journal-title":"Bioinformatics"},{"issue":"1","key":"38_CR14","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1101\/gr.1536204","volume":"14","author":"M Pop","year":"2004","unstructured":"Pop, M., Kosack, D.S., Salzberg, S.L.: Hierarchical scaffolding with bambus. Genome Res. 14(1), 149\u2013159 (2004)","journal-title":"Genome Res."},{"issue":"9","key":"38_CR15","doi-asserted-by":"crossref","first-page":"1541","DOI":"10.1101\/gr.183201","volume":"11","author":"WJ Kent","year":"2001","unstructured":"Kent, W.J., Haussler, D.: Assembly of the working draft of the human genome with gigassembler. Genome Res. 11(9), 1541\u20131548 (2001)","journal-title":"Genome Res."},{"issue":"5","key":"38_CR16","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1145\/585265.585267","volume":"49","author":"DH Huson","year":"2002","unstructured":"Huson, D.H., Reinert, K., Myers, E.W.: The greedy path-merging algorithm for contig scaffolding. J. ACM 49(5), 603\u2013615 (2002)","journal-title":"J. ACM"},{"issue":"99","key":"38_CR17","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1109\/TCBB.2016.2640303","volume":"PP","author":"L Min","year":"2016","unstructured":"Min, L., Liao, Z., He, Y., Wang, J., Luo, J., Yi, P.: Isea: iterative seed-extension algorithm for de novo assembly using paired-end information and insert size distribution. IEEE\/ACM Trans. Comput. Biol. Bioinform. PP(99), 1 (2016)","journal-title":"IEEE\/ACM Trans. Comput. Biol. Bioinform."},{"issue":"3","key":"38_CR18","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/gb-2014-15-3-r42","volume":"15","author":"M Hunt","year":"2014","unstructured":"Hunt, M., et al.: A comprehensive evaluation of assembly scaffolding tools. Genome Biol. 15(3), 1\u201315 (2014)","journal-title":"Genome Biol."},{"issue":"1","key":"38_CR19","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1186\/1471-2105-15-281","volume":"15","author":"K Sahlin","year":"2014","unstructured":"Sahlin, K., Vezzi, F., Nystedt, B., Lundeberg, J., Arvestad, L.: Besst - efficient scaffolding of large fragmented assemblies. BMC Bioinform. 15(1), 281 (2014)","journal-title":"BMC Bioinform."},{"issue":"4","key":"38_CR20","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1093\/bioinformatics\/btq683","volume":"27","author":"M Boetzer","year":"2011","unstructured":"Boetzer, M., Henkel, C.V., Jansen, H.J., Butler, D., Pirovano, W.: Scaffolding pre-assembled contigs using sspace. Bioinformatics 27(4), 578\u2013579 (2011)","journal-title":"Bioinformatics"},{"issue":"15","key":"38_CR21","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., et al.: Soap2: an improved ultrafast tool for short read alignment. Bioinformatics 25(15), 1966\u20131967 (2009)","journal-title":"Bioinformatics"}],"container-title":["Lecture Notes in Computer Science","Intelligent Computing Theories and Application"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-319-63312-1_38","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2017,7,19]],"date-time":"2017-07-19T15:53:11Z","timestamp":1500479591000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-319-63312-1_38"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017]]},"ISBN":["9783319633114","9783319633121"],"references-count":21,"URL":"https:\/\/doi.org\/10.1007\/978-3-319-63312-1_38","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2017]]}}}