{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,19]],"date-time":"2025-09-19T09:33:58Z","timestamp":1758274438969,"version":"3.40.3"},"publisher-location":"Cham","reference-count":31,"publisher":"Springer International Publishing","isbn-type":[{"type":"print","value":"9783030181734"},{"type":"electronic","value":"9783030181741"}],"license":[{"start":{"date-parts":[[2019,1,1]],"date-time":"2019-01-01T00:00:00Z","timestamp":1546300800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019]]},"DOI":"10.1007\/978-3-030-18174-1_8","type":"book-chapter","created":{"date-parts":[[2019,5,20]],"date-time":"2019-05-20T10:15:30Z","timestamp":1558347330000},"page":"112-124","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Lightweight Metagenomic Classification via eBWT"],"prefix":"10.1007","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8888-9243","authenticated-orcid":false,"given":"Veronica","family":"Guerrini","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5075-1214","authenticated-orcid":false,"given":"Giovanna","family":"Rosone","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2019,4,13]]},"reference":[{"issue":"1","key":"8_CR1","doi-asserted-by":"publisher","first-page":"53","DOI":"10.1016\/S1570-8667(03)00065-0","volume":"2","author":"MI Abouelhoda","year":"2004","unstructured":"Abouelhoda, M.I., Kurtz, S., Ohlebusch, E.: Replacing suffix trees with enhanced suffix arrays. J. Discrete Algorithms 2(1), 53\u201386 (2004)","journal-title":"J. Discrete Algorithms"},{"key":"8_CR2","doi-asserted-by":"publisher","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":"8_CR3","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1007\/978-3-319-94418-0_11","volume-title":"Sailing Routes in the World of Computation","author":"P Bonizzoni","year":"2018","unstructured":"Bonizzoni, P., Della Vedova, G., Nicosia, S., Pirola, Y., Previtali, M., Rizzi, R.: Divide and conquer computation of the multi-string BWT and LCP array. In: Manea, F., Miller, R.G., Nowotka, D. (eds.) CiE 2018. LNCS, vol. 10936, pp. 107\u2013117. Springer, Cham (2018). \n                      https:\/\/doi.org\/10.1007\/978-3-319-94418-0_11"},{"key":"8_CR4","unstructured":"Burrows, M., Wheeler, D.: A block sorting data compression algorithm. Technical report, DIGITAL System Research Center (1994)"},{"key":"8_CR5","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1016\/j.jda.2016.03.003","volume":"37","author":"A Cox","year":"2016","unstructured":"Cox, A., Garofalo, F., Rosone, G., Sciortino, M.: Lightweight LCP construction for very large collections of strings. J. Discrete Algorithms 37, 17\u201333 (2016)","journal-title":"J. Discrete Algorithms"},{"key":"8_CR6","doi-asserted-by":"crossref","unstructured":"Egidi, L., Louza, F.A., Manzini, G., Telles, G.P.: External memory BWT and LCP computation for sequence collections with applications. In: WABI 2018. LIPIcs, vol. 113, pp. 10:1\u201310:14 (2018)","DOI":"10.1186\/s13015-019-0140-0"},{"key":"8_CR7","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"176","DOI":"10.1007\/978-3-319-67428-5_15","volume-title":"String Processing and Information Retrieval","author":"L Egidi","year":"2017","unstructured":"Egidi, L., Manzini, G.: Lightweight BWT and LCP merging via the gap algorithm. In: Fici, G., Sciortino, M., Venturini, R. (eds.) SPIRE 2017. LNCS, vol. 10508, pp. 176\u2013190. Springer, Cham (2017). \n                      https:\/\/doi.org\/10.1007\/978-3-319-67428-5_15"},{"key":"8_CR8","unstructured":"Ferragina, P., Manzini, G.: Opportunistic data structures with applications. In: FOCS, pp. 390\u2013398 (2000)"},{"key":"8_CR9","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1007\/978-3-642-31265-6_21","volume-title":"Combinatorial Pattern Matching","author":"W-K Hon","year":"2012","unstructured":"Hon, W.-K., Ku, T.-H., Lu, C.-H., Shah, R., Thankachan, S.V.: Efficient algorithm for circular Burrows-Wheeler transform. In: K\u00e4rkk\u00e4inen, J., Stoye, J. (eds.) CPM 2012. LNCS, vol. 7354, pp. 257\u2013268. Springer, Heidelberg (2012). \n                      https:\/\/doi.org\/10.1007\/978-3-642-31265-6_21"},{"issue":"1","key":"8_CR10","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1093\/bioinformatics\/btt257","volume":"30","author":"L Janin","year":"2014","unstructured":"Janin, L., Rosone, G., Cox, A.J.: Adaptive reference-free compression of sequence quality scores. Bioinformatics 30(1), 24\u201330 (2014)","journal-title":"Bioinformatics"},{"issue":"12","key":"8_CR11","doi-asserted-by":"publisher","first-page":"1721","DOI":"10.1101\/gr.210641.116","volume":"26","author":"D Kim","year":"2016","unstructured":"Kim, D., Song, L., Breitwieser, F.P., Salzberg, S.L.: Centrifuge: rapid and sensitive classification of metagenomic sequences. Genome Res. 26(12), 1721\u20131729 (2016)","journal-title":"Genome Res."},{"issue":"3","key":"8_CR12","doi-asserted-by":"publisher","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","volume":"10","author":"B Langmead","year":"2009","unstructured":"Langmead, B., Trapnell, C., Pop, M., Salzberg, S.L.: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10(3), R25 (2009)","journal-title":"Genome Biol."},{"key":"8_CR13","doi-asserted-by":"crossref","unstructured":"Lindgreen, S., Adair, K.L., Gardner, P.P.: An evaluation of the accuracy and speed of metagenome analysis tools. Sci. Rep. 6, Article No. 19233 (2016)","DOI":"10.1038\/srep19233"},{"key":"8_CR14","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"285","DOI":"10.1007\/978-3-030-00479-8_23","volume-title":"String Processing and Information Retrieval","author":"FA Louza","year":"2018","unstructured":"Louza, F.A., Telles, G.P., Gog, S., Zhao, L.: Computing Burrows-Wheeler similarity distributions for string collections. In: Gagie, T., Moffat, A., Navarro, G., Cuadros-Vargas, E. (eds.) SPIRE 2018. LNCS, vol. 11147, pp. 285\u2013296. Springer, Cham (2018). \n                      https:\/\/doi.org\/10.1007\/978-3-030-00479-8_23"},{"key":"8_CR15","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1016\/j.tcs.2017.03.039","volume":"678","author":"F Louza","year":"2017","unstructured":"Louza, F., Gog, S., Telles, G.: Inducing enhanced suffix arrays for string collections. Theor. Comput. Sci. 678, 22\u201339 (2017)","journal-title":"Theor. Comput. Sci."},{"issue":"1","key":"8_CR16","doi-asserted-by":"publisher","first-page":"26","DOI":"10.1186\/s13015-017-0117-9","volume":"12","author":"F Louza","year":"2017","unstructured":"Louza, F., Telles, G., Hoffmann, S., Ciferri, C.: Generalized enhanced suffix array construction in external memory. Algorithms Mol. Biol. 12(1), 26 (2017)","journal-title":"Algorithms Mol. Biol."},{"issue":"3","key":"8_CR17","doi-asserted-by":"publisher","first-page":"298","DOI":"10.1016\/j.tcs.2007.07.014","volume":"387","author":"S Mantaci","year":"2007","unstructured":"Mantaci, S., Restivo, A., Rosone, G., Sciortino, M.: An extension of the Burrows-Wheeler transform. Theoret. Comput. Sci. 387(3), 298\u2013312 (2007)","journal-title":"Theoret. Comput. Sci."},{"issue":"3","key":"8_CR18","doi-asserted-by":"publisher","first-page":"411","DOI":"10.1007\/s00224-007-9078-6","volume":"42","author":"S Mantaci","year":"2008","unstructured":"Mantaci, S., Restivo, A., Rosone, G., Sciortino, M.: A new combinatorial approach to sequence comparison. Theory Comput. Syst. 42(3), 411\u2013429 (2008)","journal-title":"Theory Comput. Syst."},{"key":"8_CR19","doi-asserted-by":"publisher","first-page":"79","DOI":"10.1016\/j.tcs.2017.07.015","volume":"698","author":"S Mantaci","year":"2017","unstructured":"Mantaci, S., Restivo, A., Rosone, G., Sciortino, M., Versari, L.: Measuring the clustering effect of BWT via RLE. Theoret. Comput. Sci. 698, 79\u201387 (2017)","journal-title":"Theoret. Comput. Sci."},{"issue":"1","key":"8_CR20","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1016\/j.ijar.2007.03.011","volume":"47","author":"S Mantaci","year":"2008","unstructured":"Mantaci, S., Restivo, A., Sciortino, M.: Distance measures for biological sequences: some recent approaches. Int. J. Approx. Reason. 47(1), 109\u2013124 (2008)","journal-title":"Int. J. Approx. Reason."},{"issue":"1","key":"8_CR21","doi-asserted-by":"publisher","first-page":"182","DOI":"10.1186\/s13059-017-1299-7","volume":"18","author":"ABR McIntyre","year":"2017","unstructured":"McIntyre, A.B.R., et al.: Comprehensive benchmarking and ensemble approaches for metagenomic classifiers. Genome Biol. 18(1), 182 (2017)","journal-title":"Genome Biol."},{"key":"8_CR22","doi-asserted-by":"publisher","first-page":"11257","DOI":"10.1038\/ncomms11257","volume":"7","author":"P Menzel","year":"2016","unstructured":"Menzel, P., Ng, K.L., Krogh, A.: Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nature Commun. 7, 11257 (2016)","journal-title":"Nature Commun."},{"issue":"10","key":"8_CR23","doi-asserted-by":"publisher","first-page":"e47216","DOI":"10.1371\/journal.pone.0047216","volume":"7","author":"KH Ng","year":"2012","unstructured":"Ng, K.H., Ho, C.K., Phon-Amnuaisuk, S.: A hybrid distance measure for clustering expressed sequence tags originating from the same gene family. PLoS One 7(10), e47216 (2012)","journal-title":"PLoS One"},{"issue":"24","key":"8_CR24","doi-asserted-by":"publisher","first-page":"3823","DOI":"10.1093\/bioinformatics\/btw542","volume":"32","author":"R Ounit","year":"2016","unstructured":"Ounit, R., Lonardi, S.: Higher classification sensitivity of short metagenomic reads with CLARK-S. Bioinformatics 32(24), 3823\u20133825 (2016)","journal-title":"Bioinformatics"},{"issue":"1","key":"8_CR25","doi-asserted-by":"publisher","first-page":"236","DOI":"10.1186\/s12864-015-1419-2","volume":"16","author":"R Ounit","year":"2015","unstructured":"Ounit, R., Wanamaker, S., Close, T.J., Lonardi, S.: CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers. BMC Genomics 16(1), 236 (2015)","journal-title":"BMC Genomics"},{"issue":"1660","key":"8_CR26","doi-asserted-by":"publisher","first-page":"20130383","DOI":"10.1098\/rstb.2013.0383","volume":"370","author":"M Pedersen","year":"2015","unstructured":"Pedersen, M., et al.: Ancient and modern environmental DNA. Philos. Trans. R. Soc. Lond. B Biol. Sci. 370(1660), 20130383 (2015)","journal-title":"Philos. Trans. R. Soc. Lond. B Biol. Sci."},{"key":"8_CR27","unstructured":"Prezza, N., Pisanti, N., Sciortino, M., Rosone, G.: Detecting mutations by eBWT. In: WABI 2018. LIPIcs, vol. 113, pp. 3:1\u20133:15 (2018)"},{"issue":"27","key":"8_CR28","doi-asserted-by":"publisher","first-page":"3019","DOI":"10.1016\/j.tcs.2010.11.040","volume":"412","author":"A Restivo","year":"2011","unstructured":"Restivo, A., Rosone, G.: Balancing and clustering of words in the Burrows-Wheeler transform. Theoret. Comput. Sci. 412(27), 3019\u20133032 (2011)","journal-title":"Theoret. Comput. Sci."},{"issue":"4","key":"8_CR29","doi-asserted-by":"publisher","first-page":"513","DOI":"10.1093\/bioinformatics\/btg005","volume":"19","author":"S Vinga","year":"2003","unstructured":"Vinga, S., Almeida, J.: Alignment-free sequence comparison-a review. Bioinformatics 19(4), 513\u2013523 (2003)","journal-title":"Bioinformatics"},{"issue":"3","key":"8_CR30","doi-asserted-by":"publisher","first-page":"R46","DOI":"10.1186\/gb-2014-15-3-r46","volume":"15","author":"DE Wood","year":"2014","unstructured":"Wood, D.E., Salzberg, S.L.: Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol. 15(3), R46 (2014)","journal-title":"Genome Biol."},{"issue":"4","key":"8_CR31","doi-asserted-by":"publisher","first-page":"742","DOI":"10.1016\/j.jtbi.2009.10.033","volume":"262","author":"L Yang","year":"2010","unstructured":"Yang, L., Zhang, X., Wang, T.: The Burrows-Wheeler similarity distribution between biological sequences based on Burrows-Wheeler transform. J. Theor. Biol. 262(4), 742\u2013749 (2010)","journal-title":"J. Theor. Biol."}],"container-title":["Lecture Notes in Computer Science","Algorithms for Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-030-18174-1_8","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,5,22]],"date-time":"2019-05-22T16:12:31Z","timestamp":1558541551000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-030-18174-1_8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019]]},"ISBN":["9783030181734","9783030181741"],"references-count":31,"URL":"https:\/\/doi.org\/10.1007\/978-3-030-18174-1_8","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2019]]},"assertion":[{"value":"13 April 2019","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}},{"value":"AlCoB","order":1,"name":"conference_acronym","label":"Conference Acronym","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"International Conference on Algorithms for Computational Biology","order":2,"name":"conference_name","label":"Conference Name","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Berkeley, CA","order":3,"name":"conference_city","label":"Conference City","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"USA","order":4,"name":"conference_country","label":"Conference Country","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"2019","order":5,"name":"conference_year","label":"Conference Year","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"28 May 2019","order":7,"name":"conference_start_date","label":"Conference Start Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"30 May 2019","order":8,"name":"conference_end_date","label":"Conference End Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"6","order":9,"name":"conference_number","label":"Conference Number","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"alcob2019","order":10,"name":"conference_id","label":"Conference ID","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"http:\/\/alcob2019.irdta.eu\/","order":11,"name":"conference_url","label":"Conference URL","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Single-blind","order":1,"name":"type","label":"Type","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information"}},{"value":"EasyChair","order":2,"name":"conference_management_system","label":"Conference Management System","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information"}},{"value":"30","order":3,"name":"number_of_submissions_sent_for_review","label":"Number of Submissions Sent for Review","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information"}},{"value":"15","order":4,"name":"number_of_full_papers_accepted","label":"Number of Full Papers Accepted","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information"}},{"value":"0","order":5,"name":"number_of_short_papers_accepted","label":"Number of Short Papers Accepted","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information"}},{"value":"50% - The value is computed by the equation \"Number of Full Papers Accepted \/ Number of Submissions Sent for Review * 100\" and then rounded to a whole number.","order":6,"name":"acceptance_rate_of_full_papers","label":"Acceptance Rate of Full Papers","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information"}},{"value":"3","order":7,"name":"average_number_of_reviews_per_paper","label":"Average Number of Reviews per Paper","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information"}},{"value":"2","order":8,"name":"average_number_of_papers_per_reviewer","label":"Average Number of Papers per Reviewer","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information"}},{"value":"Yes","order":9,"name":"external_reviewers_involved","label":"External Reviewers Involved","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information"}},{"value":"One paper of an invited talk is included.","order":10,"name":"additional_info_on_review_process","label":"Additional Info on Review Process","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information"}}]}}