{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,26]],"date-time":"2025-03-26T22:02:39Z","timestamp":1743026559037,"version":"3.40.3"},"publisher-location":"Singapore","reference-count":39,"publisher":"Springer Nature Singapore","isbn-type":[{"type":"print","value":"9789819615247"},{"type":"electronic","value":"9789819615254"}],"license":[{"start":{"date-parts":[[2025,1,1]],"date-time":"2025-01-01T00:00:00Z","timestamp":1735689600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2025,1,1]],"date-time":"2025-01-01T00:00:00Z","timestamp":1735689600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025]]},"DOI":"10.1007\/978-981-96-1525-4_22","type":"book-chapter","created":{"date-parts":[[2025,2,16]],"date-time":"2025-02-16T09:28:17Z","timestamp":1739698097000},"page":"362-371","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["A Vectorized Sequence-to-Graph Alignment Algorithm"],"prefix":"10.1007","author":[{"ORCID":"https:\/\/orcid.org\/0009-0000-9538-485X","authenticated-orcid":false,"given":"Chenchen","family":"Peng","sequence":"first","affiliation":[]},{"given":"Shengbo","family":"Tang","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0161-8617","authenticated-orcid":false,"given":"Yifei","family":"Guo","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2816-1805","authenticated-orcid":false,"given":"Zeyu","family":"Xia","sequence":"additional","affiliation":[]},{"given":"Canqun","family":"Yang","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4000-4957","authenticated-orcid":false,"given":"Yingbo","family":"Cui","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2025,2,17]]},"reference":[{"issue":"1","key":"22_CR1","doi-asserted-by":"publisher","first-page":"48","DOI":"10.3390\/genes12010048","volume":"12","author":"M Cechova","year":"2020","unstructured":"Cechova, M.: Probably correct: rescuing repeats with short and long reads. Genes 12(1), 48 (2020)","journal-title":"Genes"},{"issue":"12","key":"22_CR2","doi-asserted-by":"publisher","first-page":"3712","DOI":"10.1093\/bioinformatics\/btaa265","volume":"36","author":"CA Darby","year":"2020","unstructured":"Darby, C.A., Gaddipati, R., Schatz, M.C., Langmead, B.: Vargas: heuristic-free alignment for assessing linear and graph read aligners. Bioinformatics 36(12), 3712\u20133718 (2020)","journal-title":"Bioinformatics"},{"issue":"4","key":"22_CR3","doi-asserted-by":"publisher","first-page":"518","DOI":"10.1038\/s41588-022-01043-w","volume":"54","author":"J Ebler","year":"2022","unstructured":"Ebler, J., et al.: Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes. Nat. Genet. 54(4), 518\u2013525 (2022)","journal-title":"Nat. Genet."},{"key":"22_CR4","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1146\/annurev-genom-120219-080406","volume":"21","author":"JM Eizenga","year":"2020","unstructured":"Eizenga, J.M., et al.: Pangenome graphs. Ann. Rev. Genomics Hum. Genet. 21, 139\u2013162 (2020)","journal-title":"Ann. Rev. Genomics Hum. Genet."},{"key":"22_CR5","doi-asserted-by":"crossref","unstructured":"Gao, Y., et\u00a0al.: A pangenome reference of 36 Chinese populations. Nature 1\u201310 (2023)","DOI":"10.1038\/s41586-023-06173-7"},{"issue":"9","key":"22_CR6","doi-asserted-by":"publisher","first-page":"875","DOI":"10.1038\/nbt.4227","volume":"36","author":"E Garrison","year":"2018","unstructured":"Garrison, E., et al.: Variation graph toolkit improves read mapping by representing genetic variation in the reference. Nat. Biotechnol. 36(9), 875\u2013879 (2018)","journal-title":"Nat. Biotechnol."},{"issue":"10","key":"22_CR7","doi-asserted-by":"publisher","first-page":"575","DOI":"10.1038\/s41576-020-0275-3","volume":"21","author":"RA Gibbs","year":"2020","unstructured":"Gibbs, R.A.: The human genome project changed everything. Nat. Rev. Genet. 21(10), 575\u2013576 (2020)","journal-title":"Nat. Rev. Genet."},{"issue":"5979","key":"22_CR8","doi-asserted-by":"publisher","first-page":"710","DOI":"10.1126\/science.1188021","volume":"328","author":"RE Green","year":"2010","unstructured":"Green, R.E., et al.: A draft sequence of the Neandertal genome. Science 328(5979), 710\u2013722 (2010)","journal-title":"Science"},{"key":"22_CR9","doi-asserted-by":"crossref","unstructured":"Guo, Y., et al.: MTMap: a long-read alignment tool based on multi-core DSPs. In: 2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 863\u2013866. IEEE (2023)","DOI":"10.1109\/BIBM58861.2023.10385767"},{"key":"22_CR10","doi-asserted-by":"crossref","unstructured":"Jain, C., Misra, S., Zhang, H., Dilthey, A., Aluru, S.: Accelerating sequence alignment to graphs. In: 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS), pp. 451\u2013461. IEEE (2019)","DOI":"10.1109\/IPDPS.2019.00055"},{"key":"22_CR11","unstructured":"Lander, E.S., et\u00a0al.: C. International human genome sequencing. In: Initial Sequencing and Analysis of the Human Genome, pp. 860\u2013921 (2001)"},{"issue":"3","key":"22_CR12","doi-asserted-by":"publisher","first-page":"452","DOI":"10.1093\/bioinformatics\/18.3.452","volume":"18","author":"C Lee","year":"2002","unstructured":"Lee, C., Grasso, C., Sharlow, M.F.: Multiple sequence alignment using partial order graphs. Bioinformatics 18(3), 452\u2013464 (2002)","journal-title":"Bioinformatics"},{"issue":"14","key":"22_CR13","doi-asserted-by":"publisher","first-page":"2103","DOI":"10.1093\/bioinformatics\/btw152","volume":"32","author":"H Li","year":"2016","unstructured":"Li, H.: Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences. Bioinformatics 32(14), 2103\u20132110 (2016)","journal-title":"Bioinformatics"},{"issue":"18","key":"22_CR14","doi-asserted-by":"publisher","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","volume":"34","author":"H Li","year":"2018","unstructured":"Li, H.: Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34(18), 3094\u20133100 (2018)","journal-title":"Bioinformatics"},{"key":"22_CR15","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13059-020-02168-z","volume":"21","author":"H Li","year":"2020","unstructured":"Li, H., Feng, X., Chu, C.: The design and construction of reference pangenome graphs with minigraph. Genome Biol. 21, 1\u201319 (2020)","journal-title":"Genome Biol."},{"issue":"7960","key":"22_CR16","doi-asserted-by":"publisher","first-page":"312","DOI":"10.1038\/s41586-023-05896-x","volume":"617","author":"W-W Liao","year":"2023","unstructured":"Liao, W.-W., et al.: A draft human pangenome reference. Nature 617(7960), 312\u2013324 (2023)","journal-title":"Nature"},{"issue":"4","key":"22_CR17","doi-asserted-by":"publisher","first-page":"456","DOI":"10.1093\/bioinformatics\/btaa777","volume":"37","author":"S Marco-Sola","year":"2021","unstructured":"Marco-Sola, S., Moure, J.C., Moreto, M., Espinosa, A.: Fast gap-affine pairwise alignment using the wavefront algorithm. Bioinformatics 37(4), 456\u2013463 (2021)","journal-title":"Bioinformatics"},{"key":"22_CR18","doi-asserted-by":"crossref","unstructured":"Marco-Sola, S., Eizenga, J.M., Guarracino, A., Paten, B., Garrison, E., Moreto, M.: Optimal gap-affine alignment in $$O(s)$$ space. Bioinformatics 39(2), btad074 (2023)","DOI":"10.1093\/bioinformatics\/btad074"},{"key":"22_CR19","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1146\/annurev-genom-120120-081921","volume":"22","author":"KH Miga","year":"2021","unstructured":"Miga, K.H., Wang, T.: The need for a human pangenome reference sequence. Ann. Rev. Genomics Hum. Genet. 22, 81\u2013102 (2021)","journal-title":"Ann. Rev. Genomics Hum. Genet."},{"issue":"1\u20134","key":"22_CR20","doi-asserted-by":"publisher","first-page":"251","DOI":"10.1007\/BF01840446","volume":"1","author":"EW Myers","year":"1986","unstructured":"Myers, E.W.: An $$O (ND)$$ difference algorithm and its variations. Algorithmica 1(1\u20134), 251\u2013266 (1986)","journal-title":"Algorithmica"},{"issue":"1\u20132","key":"22_CR21","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1016\/S0304-3975(99)00333-3","volume":"237","author":"G Navarro","year":"2000","unstructured":"Navarro, G.: Improved approximate pattern matching on hypertext. Theor. Comput. Sci. 237(1\u20132), 455\u2013463 (2000)","journal-title":"Theor. Comput. Sci."},{"issue":"3","key":"22_CR22","doi-asserted-by":"publisher","first-page":"443","DOI":"10.1016\/0022-2836(70)90057-4","volume":"48","author":"SB Needleman","year":"1970","unstructured":"Needleman, S.B., Wunsch, C.D.: A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48(3), 443\u2013453 (1970)","journal-title":"J. Mol. Biol."},{"issue":"6588","key":"22_CR23","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1126\/science.abj6987","volume":"376","author":"S Nurk","year":"2022","unstructured":"Nurk, S., et al.: The complete sequence of a human genome. Science 376(6588), 44\u201353 (2022)","journal-title":"Science"},{"issue":"5","key":"22_CR24","doi-asserted-by":"publisher","first-page":"589","DOI":"10.1093\/bioinformatics\/btaa835","volume":"37","author":"Y Ono","year":"2021","unstructured":"Ono, Y., Asai, K., Hamada, M.: PBSIM2: a simulator for long-read sequencers with a novel generative model of quality scores. Bioinformatics 37(5), 589\u2013595 (2021)","journal-title":"Bioinformatics"},{"issue":"1","key":"22_CR25","doi-asserted-by":"publisher","first-page":"253","DOI":"10.1186\/s13059-020-02157-2","volume":"21","author":"M Rautiainen","year":"2020","unstructured":"Rautiainen, M., Marschall, T.: GraphAligner: rapid and versatile sequence-to-graph alignment. Genome Biol. 21(1), 253 (2020)","journal-title":"Genome Biol."},{"issue":"19","key":"22_CR26","doi-asserted-by":"publisher","first-page":"3599","DOI":"10.1093\/bioinformatics\/btz162","volume":"35","author":"M Rautiainen","year":"2019","unstructured":"Rautiainen, M., M\u00e4kinen, V., Marschall, T.: Bit-parallel sequence-to-graph alignment. Bioinformatics 35(19), 3599\u20133607 (2019)","journal-title":"Bioinformatics"},{"issue":"7856","key":"22_CR27","doi-asserted-by":"publisher","first-page":"737","DOI":"10.1038\/s41586-021-03451-0","volume":"592","author":"A Rhie","year":"2021","unstructured":"Rhie, A., et al.: Towards complete and error-free genome assemblies of all vertebrate species. Nature 592(7856), 737\u2013746 (2021)","journal-title":"Nature"},{"issue":"1","key":"22_CR28","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13059-023-02972-3","volume":"24","author":"K Sahlin","year":"2023","unstructured":"Sahlin, K., Baudeau, T., Cazaux, B., Marchet, C.: A survey of mapping algorithms in the long-reads era. Genome Biol. 24(1), 1\u201323 (2023)","journal-title":"Genome Biol."},{"issue":"5","key":"22_CR29","doi-asserted-by":"publisher","first-page":"849","DOI":"10.1101\/gr.213611.116","volume":"27","author":"VA Schneider","year":"2017","unstructured":"Schneider, V.A., et al.: Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly. Genome Res. 27(5), 849\u2013864 (2017)","journal-title":"Genome Res."},{"issue":"4","key":"22_CR30","doi-asserted-by":"publisher","first-page":"243","DOI":"10.1038\/s41576-020-0210-7","volume":"21","author":"RM Sherman","year":"2020","unstructured":"Sherman, R.M., Salzberg, S.L.: Pan-genomics in the human genome era. Nat. Rev. Genet. 21(4), 243\u2013254 (2020)","journal-title":"Nat. Rev. Genet."},{"key":"22_CR31","doi-asserted-by":"crossref","unstructured":"Sir\u00e9n, J., et al.: Pangenomics enables genotyping of known structural variants in 5202 diverse genomes. Science 374(6574), abg8871 (2021)","DOI":"10.1126\/science.abg8871"},{"issue":"1","key":"22_CR32","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1016\/0022-2836(81)90087-5","volume":"147","author":"TF Smith","year":"1981","unstructured":"Smith, T.F., Waterman, M.S., et al.: Identification of common molecular subsequences. J. Mol. Biol. 147(1), 195\u2013197 (1981)","journal-title":"J. Mol. Biol."},{"issue":"5507","key":"22_CR33","doi-asserted-by":"publisher","first-page":"1304","DOI":"10.1126\/science.1058040","volume":"291","author":"JC Venter","year":"2001","unstructured":"Venter, J.C., et al.: The sequence of the human genome. Science 291(5507), 1304\u20131351 (2001)","journal-title":"Science"},{"issue":"7906","key":"22_CR34","doi-asserted-by":"publisher","first-page":"437","DOI":"10.1038\/s41586-022-04601-8","volume":"604","author":"T Wang","year":"2022","unstructured":"Wang, T., et al.: The human pangenome project: a global resource to map genomic diversity. Nature 604(7906), 437\u2013446 (2022)","journal-title":"Nature"},{"issue":"10","key":"22_CR35","doi-asserted-by":"publisher","first-page":"1155","DOI":"10.1038\/s41587-019-0217-9","volume":"37","author":"AM Wenger","year":"2019","unstructured":"Wenger, A.M., et al.: Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome. Nat. Biotechnol. 37(10), 1155\u20131162 (2019)","journal-title":"Nat. Biotechnol."},{"key":"22_CR36","doi-asserted-by":"crossref","unstructured":"Xia, Z., et al.: A review of parallel implementations for the Smith\u2013Waterman algorithm. Interdisc. Sci. Comput. Life Sci. 1\u201314 (2021)","DOI":"10.1007\/s12539-021-00473-0"},{"key":"22_CR37","doi-asserted-by":"crossref","unstructured":"Xia, Z., et al.: Large-scale parallel alignment algorithm for SMRT reads. In: International Conference on Algorithms and Architectures for Parallel Processing, pp. 213\u2013229. Springer (2021)","DOI":"10.1007\/978-3-030-95388-1_14"},{"key":"22_CR38","unstructured":"Zhang, H., Wu, S., Aluru, S., Li, H.: Fast sequence to graph alignment using the graph wavefront algorithm. arXiv preprint arXiv:2206.13574 (2022)"},{"issue":"1\u20132","key":"22_CR39","doi-asserted-by":"publisher","first-page":"203","DOI":"10.1089\/10665270050081478","volume":"7","author":"Z Zhang","year":"2000","unstructured":"Zhang, Z., Schwartz, S., Wagner, L., Miller, W.: A greedy algorithm for aligning DNA sequences. J. Comput. Biol. 7(1\u20132), 203\u2013214 (2000)","journal-title":"J. Comput. Biol."}],"container-title":["Lecture Notes in Computer Science","Algorithms and Architectures for Parallel Processing"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-981-96-1525-4_22","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,2,16]],"date-time":"2025-02-16T09:28:32Z","timestamp":1739698112000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-981-96-1525-4_22"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025]]},"ISBN":["9789819615247","9789819615254"],"references-count":39,"URL":"https:\/\/doi.org\/10.1007\/978-981-96-1525-4_22","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2025]]},"assertion":[{"value":"17 February 2025","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}},{"value":"ICA3PP","order":1,"name":"conference_acronym","label":"Conference Acronym","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"International Conference on Algorithms and Architectures for Parallel Processing","order":2,"name":"conference_name","label":"Conference Name","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Macau","order":3,"name":"conference_city","label":"Conference City","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"China","order":4,"name":"conference_country","label":"Conference Country","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"2024","order":5,"name":"conference_year","label":"Conference Year","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"30 October 2024","order":7,"name":"conference_start_date","label":"Conference Start Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"1 November 2024","order":8,"name":"conference_end_date","label":"Conference End Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"24","order":9,"name":"conference_number","label":"Conference Number","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"ica3pp2024","order":10,"name":"conference_id","label":"Conference ID","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"https:\/\/ica3pp2024.scimeeting.cn\/en\/web\/index\/","order":11,"name":"conference_url","label":"Conference URL","group":{"name":"ConferenceInfo","label":"Conference Information"}}]}}