{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,28]],"date-time":"2026-02-28T07:54:47Z","timestamp":1772265287675,"version":"3.50.1"},"publisher-location":"Cham","reference-count":24,"publisher":"Springer International Publishing","isbn-type":[{"value":"9783030800482","type":"print"},{"value":"9783030800499","type":"electronic"}],"license":[{"start":{"date-parts":[[2021,1,1]],"date-time":"2021-01-01T00:00:00Z","timestamp":1609459200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springer.com\/tdm"},{"start":{"date-parts":[[2021,1,1]],"date-time":"2021-01-01T00:00:00Z","timestamp":1609459200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021]]},"DOI":"10.1007\/978-3-030-80049-9_15","type":"book-chapter","created":{"date-parts":[[2021,7,1]],"date-time":"2021-07-01T18:06:14Z","timestamp":1625162774000},"page":"169-177","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Walk-Preserving Transformation of Overlapped Sequence Graphs into Blunt Sequence Graphs with GetBlunted"],"prefix":"10.1007","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8345-8356","authenticated-orcid":false,"given":"Jordan M.","family":"Eizenga","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8183-9611","authenticated-orcid":false,"given":"Ryan","family":"Lorig-Roach","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5736-3193","authenticated-orcid":false,"given":"Melissa M.","family":"Meredith","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8863-3539","authenticated-orcid":false,"given":"Benedict","family":"Paten","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2021,7,2]]},"reference":[{"issue":"2\u20133","key":"15_CR1","doi-asserted-by":"publisher","first-page":"125","DOI":"10.1016\/S0166-218X(98)00039-0","volume":"86","author":"J Amilhastre","year":"1998","unstructured":"Amilhastre, J., Vilarem, M.C., Janssen, P.: Complexity of minimum biclique cover and minimum biclique decomposition for bipartite domino-free graphs. Discret. Appl. Math. 86(2\u20133), 125\u2013144 (1998)","journal-title":"Discret. Appl. Math."},{"key":"15_CR2","doi-asserted-by":"publisher","unstructured":"Bankevich, A., Bzikadze, A., Kolmogorov, M., Pevzner, P.A.: Assembling Long Accurate Reads Using de Bruijn Graphs. bioRxiv p. 2020.12.10.420448 (December 2020). https:\/\/doi.org\/10.1101\/2020.12.10.420448, https:\/\/www.biorxiv.org\/content\/10.1101\/2020.12.10.420448v1, publisher: Cold Spring Harbor Laboratory Section: New Results","DOI":"10.1101\/2020.12.10.420448"},{"issue":"1\u20133","key":"15_CR3","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1016\/S0012-365X(98)00115-0","volume":"194","author":"S Bylka","year":"1999","unstructured":"Bylka, S., Idzik, A., Tuza, Z.: Maximum cuts: improvements and local algorithmic analogues of the Edwards-Erdos inequality. Discret. Math. 194(1\u20133), 39\u201358 (1999)","journal-title":"Discret. Math."},{"key":"15_CR4","unstructured":"Computational Pan-Genomics Consortium: Computational pan-genomics: status, promises and challenges. Brief. Bioinform. 19(1), 118\u2013135 (2018)"},{"key":"15_CR5","doi-asserted-by":"crossref","unstructured":"Dawson, E.T., Durbin, R.: GFAKluge: A C++ library and command line utilities for the graphical fragment assembly formats. J. Open Source Softw. 4(33), 1083 (2019)","DOI":"10.21105\/joss.01083"},{"key":"15_CR6","doi-asserted-by":"crossref","unstructured":"Eizenga, J.M., et al.: Efficient dynamic variation graphs. Bioinformatics 36(21), 5139\u20135144 (2020)","DOI":"10.1093\/bioinformatics\/btaa640"},{"key":"15_CR7","doi-asserted-by":"crossref","unstructured":"Ene, A., Horne, W., Milosavljevic, N., Rao, P., Schreiber, R., Tarjan, R.E.: Fast exact and heuristic methods for role minimization problems. In: Proceedings of the 13th ACM Symposium on Access Control Models and Technologies, pp. 1\u201310 (2008)","DOI":"10.1145\/1377836.1377838"},{"key":"15_CR8","unstructured":"Garrison, E.: ekg\/gimbricate. https:\/\/github.com\/ekg\/gimbricate (October 2020)"},{"key":"15_CR9","unstructured":"Garrison, E.: ekg\/seqwish. https:\/\/github.com\/ekg\/seqwish (February 2021)"},{"issue":"9","key":"15_CR10","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":"1","key":"15_CR11","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2105-7-541","volume":"7","author":"B Haubold","year":"2006","unstructured":"Haubold, B., Wiehe, T.: How repetitive are genomes? BMC Bioinform. 7(1), 1\u201310 (2006)","journal-title":"BMC Bioinform."},{"key":"15_CR12","doi-asserted-by":"publisher","unstructured":"Jain, C., Zhang, H., Gao, Y., Aluru, S.: On the complexity of sequence to graph alignment. bioRxiv (January 2019). https:\/\/doi.org\/10.1101\/522912","DOI":"10.1101\/522912"},{"key":"15_CR13","doi-asserted-by":"publisher","unstructured":"Karp, R.M.: Reducibility among combinatorial problems. In: Miller R.E., Thatcher J.W., Bohlinger J.D. (eds.) Complexity of Computer Computations, pp. 85\u2013103. Springer, Boston (1972) https:\/\/doi.org\/10.1007\/978-1-4684-2001-2_9","DOI":"10.1007\/978-1-4684-2001-2_9"},{"issue":"3","key":"15_CR14","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"},{"key":"15_CR15","unstructured":"Li, H., et al.: GFA specification (2013). https:\/\/github.com\/GFA-spec\/GFA-spec"},{"issue":"2","key":"15_CR16","doi-asserted-by":"publisher","first-page":"275","DOI":"10.1089\/cmb.1995.2.275","volume":"2","author":"EW Myers","year":"1995","unstructured":"Myers, E.W.: Toward simplifying and accurately formulating fragment assembly. J. Comput. Biol. 2(2), 275\u2013290 (1995)","journal-title":"J. Comput. Biol."},{"key":"15_CR17","doi-asserted-by":"crossref","unstructured":"Myers, E.W.: The fragment assembly string graph. Bioinformatics 21(suppl 2), ii79\u2013ii85 (2005)","DOI":"10.1093\/bioinformatics\/bti1114"},{"key":"15_CR18","unstructured":"Nikaein, H.: hnikaein\/stark (January 2021). https:\/\/github.com\/hnikaein\/stark"},{"key":"15_CR19","doi-asserted-by":"crossref","unstructured":"Orlin, J., et al.: Contentment in graph theory: covering graphs with cliques. In: Indagationes Mathematicae (Proceedings), vol. 80, pp. 406\u2013424. North-Holland (1977)","DOI":"10.1016\/1385-7258(77)90055-5"},{"issue":"17","key":"15_CR20","doi-asserted-by":"publisher","first-page":"9748","DOI":"10.1073\/pnas.171285098","volume":"98","author":"PA Pevzner","year":"2001","unstructured":"Pevzner, P.A., Tang, H., Waterman, M.S.: An Eulerian path approach to DNA fragment assembly. Proc. Natl. Acad. Sci. 98(17), 9748\u20139753 (2001)","journal-title":"Proc. Natl. Acad. Sci."},{"key":"15_CR21","doi-asserted-by":"crossref","unstructured":"Rautiainen, M., Marschall, T.: Aligning sequences to general graphs in O(V+ mE) time. bioRxiv p. 216127 (2017)","DOI":"10.1101\/216127"},{"issue":"1","key":"15_CR22","doi-asserted-by":"publisher","first-page":"1","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), 1\u201328 (2020)","journal-title":"Genome Biol."},{"key":"15_CR23","doi-asserted-by":"publisher","unstructured":"Shafin, K., et al.: Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes. Nature Biotechnology 38(9), 1044\u20131053 (2020). https:\/\/doi.org\/10.1038\/s41587-020-0503-6, https:\/\/www.nature.com\/articles\/s41587-020-0503-6. number: 9 Publisher: Nature Publishing Group","DOI":"10.1038\/s41587-020-0503-6"},{"issue":"5","key":"15_CR24","doi-asserted-by":"publisher","first-page":"737","DOI":"10.1101\/gr.214270.116","volume":"27","author":"R Vaser","year":"2017","unstructured":"Vaser, R., Sovi\u0107, I., Nagarajan, N., \u0160iki\u0107, M.: Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res. 27(5), 737\u2013746 (2017)","journal-title":"Genome Res."}],"container-title":["Lecture Notes in Computer Science","Connecting with Computability"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-030-80049-9_15","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,12,6]],"date-time":"2021-12-06T17:05:20Z","timestamp":1638810320000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-3-030-80049-9_15"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021]]},"ISBN":["9783030800482","9783030800499"],"references-count":24,"URL":"https:\/\/doi.org\/10.1007\/978-3-030-80049-9_15","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"value":"0302-9743","type":"print"},{"value":"1611-3349","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021]]},"assertion":[{"value":"2 July 2021","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}},{"value":"CiE","order":1,"name":"conference_acronym","label":"Conference Acronym","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Conference on Computability in Europe","order":2,"name":"conference_name","label":"Conference Name","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"2021","order":5,"name":"conference_year","label":"Conference Year","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"5 July 2021","order":7,"name":"conference_start_date","label":"Conference Start Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"9 July 2021","order":8,"name":"conference_end_date","label":"Conference End Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"17","order":9,"name":"conference_number","label":"Conference Number","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"cie2021","order":10,"name":"conference_id","label":"Conference ID","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"https:\/\/www.cie2021.ugent.be\/","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 (provided by the conference organizers)"}},{"value":"Easychair","order":2,"name":"conference_management_system","label":"Conference Management System","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"50","order":3,"name":"number_of_submissions_sent_for_review","label":"Number of Submissions Sent for Review","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"28","order":4,"name":"number_of_full_papers_accepted","label":"Number of Full Papers Accepted","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"0","order":5,"name":"number_of_short_papers_accepted","label":"Number of Short Papers Accepted","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"56% - 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 (provided by the conference organizers)"}},{"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 (provided by the conference organizers)"}},{"value":"6","order":8,"name":"average_number_of_papers_per_reviewer","label":"Average Number of Papers per Reviewer","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"Yes","order":9,"name":"external_reviewers_involved","label":"External Reviewers Involved","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}}]}}