{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,9]],"date-time":"2024-09-09T04:41:12Z","timestamp":1725856872212},"publisher-location":"Cham","reference-count":25,"publisher":"Springer International Publishing","isbn-type":[{"type":"print","value":"9783319387819"},{"type":"electronic","value":"9783319387826"}],"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\/978-3-319-38782-6_3","type":"book-chapter","created":{"date-parts":[[2016,5,26]],"date-time":"2016-05-26T13:05:32Z","timestamp":1464267932000},"page":"27-39","source":"Crossref","is-referenced-by-count":1,"title":["FSG: Fast String Graph Construction for De Novo Assembly of Reads Data"],"prefix":"10.1007","author":[{"given":"Paola","family":"Bonizzoni","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gianluca","family":"Della Vedova","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuri","family":"Pirola","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marco","family":"Previtali","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Raffaella","family":"Rizzi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2016,5,27]]},"reference":[{"issue":"5","key":"3_CR1","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","volume":"19","author":"A Bankevich","year":"2012","unstructured":"Bankevich, A., Nurk, S., et al.: SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19(5), 455\u2013477 (2012)","journal-title":"J. Comput. Biol."},{"key":"3_CR2","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1016\/j.tcs.2012.02.002","volume":"483","author":"M Bauer","year":"2013","unstructured":"Bauer, M., Cox, A., Rosone, G.: Lightweight algorithms for constructing and inverting the BWT of string collections. Theoret. Comput. Sci. 483, 134\u2013148 (2013)","journal-title":"Theoret. Comput. Sci."},{"key":"3_CR3","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"crossref","first-page":"326","DOI":"10.1007\/978-3-642-33122-0_26","volume-title":"Algorithms in Bioinformatics","author":"MJ Bauer","year":"2012","unstructured":"Bauer, M.J., Cox, A.J., Rosone, G., Sciortino, M.: Lightweight LCP construction for next-generation sequencing datasets. In: Raphael, B., Tang, J. (eds.) WABI 2012. LNCS, vol. 7534, pp. 326\u2013337. Springer, Heidelberg (2012)"},{"issue":"24","key":"3_CR4","doi-asserted-by":"crossref","first-page":"3515","DOI":"10.1093\/bioinformatics\/btu578","volume":"30","author":"I Ben-Bassat","year":"2014","unstructured":"Ben-Bassat, I., Chor, B.: String graph construction using incremental hashing. Bioinformatics 30(24), 3515\u20133523 (2014)","journal-title":"Bioinformatics"},{"issue":"1","key":"3_CR5","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1089\/cmb.2013.0112","volume":"16","author":"S Beretta","year":"2014","unstructured":"Beretta, S., Bonizzoni, P., Della Vedova, G., Pirola, Y., Rizzi, R.: Modeling alternative splicing variants from RNA-Seq data with isoform graphs. J. Comput. Biol. 16(1), 16\u201340 (2014)","journal-title":"J. Comput. Biol."},{"issue":"6","key":"3_CR6","doi-asserted-by":"crossref","first-page":"675","DOI":"10.1007\/BF02945456","volume":"18","author":"P Bonizzoni","year":"2003","unstructured":"Bonizzoni, P., Della Vedova, G., Dondi, R., Li, J.: The haplotyping problem: an overview of computational models and solutions. J. Comput. Sci. Technol. 18(6), 675\u2013688 (2003)","journal-title":"J. Comput. Sci. Technol."},{"key":"3_CR7","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1007\/978-3-662-44753-6_23","volume-title":"Algorithms in Bioinformatics","author":"P Bonizzoni","year":"2014","unstructured":"Bonizzoni, P., Della Vedova, G., Pirola, Y., Previtali, M., Rizzi, R.: Constructing string graphs in external memory. In: Brown, D., Morgenstern, B. (eds.) WABI 2014. LNCS, vol. 8701, pp. 311\u2013325. Springer, Heidelberg (2014)"},{"issue":"3","key":"3_CR8","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1089\/cmb.2015.0172","volume":"23","author":"P Bonizzoni","year":"2016","unstructured":"Bonizzoni, P., Della Vedova, G., Pirola, Y., Previtali, M., Rizzi, R.: LSG: an external-memory tool to compute string graphs for NGS data assembly. J. Comp. Biol. 23(3), 137\u2013149 (2016)","journal-title":"J. Comp. Biol."},{"key":"3_CR9","doi-asserted-by":"crossref","unstructured":"Boucher, C., Bowe, A., Gagie, T., et al.: Variable-order de bruijn graphs. In: 2015 Data Compression Conference (DCC), pp. 383\u2013392. IEEE (2015)","DOI":"10.1109\/DCC.2015.70"},{"issue":"1","key":"3_CR10","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/2047-217X-2-10","volume":"2","author":"KR Bradnam","year":"2013","unstructured":"Bradnam, K.R., Fass, J.N., Alexandrov, A., et al.: Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. GigaScience 2(1), 1\u201331 (2013)","journal-title":"GigaScience"},{"key":"3_CR11","unstructured":"Burrows, M., Wheeler, D.J.: A block-sorting lossless data compression algorithm. Technical report, Digital Systems Research Center (1994)"},{"issue":"5","key":"3_CR12","doi-asserted-by":"crossref","first-page":"336","DOI":"10.1089\/cmb.2014.0160","volume":"22","author":"R Chikhi","year":"2015","unstructured":"Chikhi, R., Limasset, A., Jackman, S., Simpson, J.T., Medvedev, P.: On the representation of de bruijn graphs. J. Comp. Biol. 22(5), 336\u2013352 (2015)","journal-title":"J. Comp. Biol."},{"issue":"22","key":"3_CR13","first-page":"1","volume":"8","author":"R Chikhi","year":"2013","unstructured":"Chikhi, R., Rizk, G.: Space-efficient and exact de Bruijn graph representation based on a Bloom filter. Alg. Mol. Biol. 8(22), 1\u20139 (2013)","journal-title":"Alg. Mol. Biol."},{"issue":"4","key":"3_CR14","doi-asserted-by":"crossref","first-page":"552","DOI":"10.1145\/1082036.1082039","volume":"52","author":"P Ferragina","year":"2005","unstructured":"Ferragina, P., Manzini, G.: Indexing compressed text. J. ACM 52(4), 552\u2013581 (2005)","journal-title":"J. ACM"},{"issue":"1","key":"3_CR15","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1186\/1471-2105-13-82","volume":"13","author":"G Gonnella","year":"2012","unstructured":"Gonnella, G., Kurtz, S.: Readjoiner: a fast and memory efficient string graph-based sequence assembler. BMC Bioinform. 13(1), 82 (2012)","journal-title":"BMC Bioinform."},{"key":"3_CR16","series-title":"Lecture Notes in Computer Science (Lecture Notes in Bioinformatics)","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1007\/978-3-540-87361-7_5","volume-title":"Algorithms in Bioinformatics","author":"V Lacroix","year":"2008","unstructured":"Lacroix, V., Sammeth, M., Guigo, R., Bergeron, A.: Exact transcriptome reconstruction from short sequence reads. In: Crandall, K.A., Lagergren, J. (eds.) WABI 2008. LNCS (LNBI), vol. 5251, pp. 50\u201363. Springer, Heidelberg (2008)"},{"issue":"14","key":"3_CR17","doi-asserted-by":"crossref","first-page":"1838","DOI":"10.1093\/bioinformatics\/bts280","volume":"28","author":"H Li","year":"2012","unstructured":"Li, H.: Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly. Bioinformatics 28(14), 1838\u20131844 (2012)","journal-title":"Bioinformatics"},{"issue":"s2","key":"3_CR18","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1093\/bioinformatics\/bti1114","volume":"21","author":"E Myers","year":"2005","unstructured":"Myers, E.: The fragment assembly string graph. Bioinformatics 21(s2), 79\u201385 (2005)","journal-title":"Bioinformatics"},{"issue":"11","key":"3_CR19","doi-asserted-by":"crossref","first-page":"1420","DOI":"10.1093\/bioinformatics\/bts174","volume":"28","author":"Y Peng","year":"2012","unstructured":"Peng, Y., Leung, H.C., Yiu, S.-M., Chin, F.: IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28(11), 1420\u20131428 (2012)","journal-title":"Bioinformatics"},{"issue":"1","key":"3_CR20","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1186\/1748-7188-9-2","volume":"9","author":"K Salikhov","year":"2014","unstructured":"Salikhov, K., Sacomoto, G., Kucherov, G.: Using cascading bloom filters to improve the memory usage for de brujin graphs. Alg. Mol. Biol. 9(1), 2 (2014)","journal-title":"Alg. Mol. Biol."},{"issue":"3","key":"3_CR21","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1101\/gr.131383.111","volume":"22","author":"SL Salzberg","year":"2012","unstructured":"Salzberg, S.L., et al.: GAGE: a critical evaluation of genome assemblies and assembly algorithms. Genome Res. 22(3), 557\u2013567 (2012)","journal-title":"Genome Res."},{"key":"3_CR22","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1007\/BFb0027775","volume-title":"Concurrency and Parallelism, Programming, Networking, and Security","author":"F Shi","year":"1996","unstructured":"Shi, F.: Suffix arrays for multiple strings: a method for on-line multiple string searches. In: Jaffar, J., Yap, R.H.C. (eds.) ASIAN 1996. LNCS, vol. 1179, pp. 11\u201322. Springer, Heidelberg (1996)"},{"issue":"12","key":"3_CR23","doi-asserted-by":"crossref","first-page":"i367","DOI":"10.1093\/bioinformatics\/btq217","volume":"26","author":"J Simpson","year":"2010","unstructured":"Simpson, J., Durbin, R.: Efficient construction of an assembly string graph using the FM-index. Bioinformatics 26(12), i367\u2013i373 (2010)","journal-title":"Bioinformatics"},{"key":"3_CR24","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1101\/gr.126953.111","volume":"22","author":"J Simpson","year":"2012","unstructured":"Simpson, J., Durbin, R.: Efficient de novo assembly of large genomes using compressed data structures. Genome Res. 22, 549\u2013556 (2012)","journal-title":"Genome Res."},{"issue":"6","key":"3_CR25","doi-asserted-by":"crossref","first-page":"1117","DOI":"10.1101\/gr.089532.108","volume":"19","author":"J Simpson","year":"2009","unstructured":"Simpson, J., Wong, K., Jackman, S., et al.: ABySS: a parallel assembler for short read sequence data. Genome Res. 19(6), 1117\u20131123 (2009)","journal-title":"Genome Res."}],"container-title":["Lecture Notes in Computer Science","Bioinformatics Research and Applications"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-319-38782-6_3","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,17]],"date-time":"2024-06-17T04:34:11Z","timestamp":1718598851000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-319-38782-6_3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016]]},"ISBN":["9783319387819","9783319387826"],"references-count":25,"URL":"https:\/\/doi.org\/10.1007\/978-3-319-38782-6_3","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2016]]}}}