{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,26]],"date-time":"2025-10-26T14:33:50Z","timestamp":1761489230133},"reference-count":20,"publisher":"Springer Science and Business Media LLC","issue":"S15","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2013,10]]},"DOI":"10.1186\/1471-2105-14-s15-s16","type":"journal-article","created":{"date-parts":[[2013,10,15]],"date-time":"2013-10-15T09:02:53Z","timestamp":1381827773000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":39,"title":["Finishing bacterial genome assemblies with Mix"],"prefix":"10.1186","volume":"14","author":[{"given":"Hayssam","family":"Soueidan","sequence":"first","affiliation":[]},{"given":"Florence","family":"Maurier","sequence":"additional","affiliation":[]},{"given":"Alexis","family":"Groppi","sequence":"additional","affiliation":[]},{"given":"Pascal","family":"Sirand-Pugnet","sequence":"additional","affiliation":[]},{"given":"Florence","family":"Tardy","sequence":"additional","affiliation":[]},{"given":"Christine","family":"Citti","sequence":"additional","affiliation":[]},{"given":"Virginie","family":"Dupuy","sequence":"additional","affiliation":[]},{"given":"Macha","family":"Nikolski","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2013,10,15]]},"reference":[{"issue":"6","key":"6110_CR1","doi-asserted-by":"publisher","first-page":"1147","DOI":"10.1101\/gr.1917404","volume":"14","author":"B Chevreux","year":"2004","unstructured":"Chevreux B, Pfisterer T, Drescher B, Driesel A, Muller W, Wetter T, Suhai S: Using the MiraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res. 2004, 14 (6): 1147-59. 10.1101\/gr.1917404.","journal-title":"Genome Res"},{"issue":"6","key":"6110_CR2","doi-asserted-by":"publisher","first-page":"1117","DOI":"10.1101\/gr.089532.108","volume":"19","author":"J Simpson","year":"2009","unstructured":"Simpson J, Wong K, Jackman S, Schein J, Jones S, Birol I: ABySS: a parallel assembler for short read sequence data. Genome Res. 2009, 19 (6): 1117-23. 10.1101\/gr.089532.108.","journal-title":"Genome Res"},{"issue":"3","key":"6110_CR3","doi-asserted-by":"publisher","first-page":"R31","DOI":"10.1186\/gb-2011-12-3-r31","volume":"12","author":"L Ye","year":"2011","unstructured":"Ye L, Hillier L, Minx P, Thane N, Locke D, Martin J, Chen L, Mitreva M, Miller J, Haub K, Dooling D, Mardis E, Wilson R, Weinstock G, Warren W: A vertebrate case study of the quality of assemblies derived from next-generation sequences. Genome Biol. 2011, 12 (3): R31-10.1186\/gb-2011-12-3-r31.","journal-title":"Genome Biol"},{"key":"6110_CR4","doi-asserted-by":"publisher","first-page":"R32","DOI":"10.1186\/gb-2009-10-3-r32","volume":"10","author":"O Harismendy","year":"2009","unstructured":"Harismendy O, Ng P, Strausberg R, Wang X, Stockwell T, Beeson K, Schork N, Murray S, Topol E, Levy S, Frazer K: Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol. 2009, 10: R32-10.1186\/gb-2009-10-3-r32.","journal-title":"Genome Biol"},{"key":"6110_CR5","doi-asserted-by":"publisher","first-page":"R94","DOI":"10.1186\/gb-2009-10-9-r94","volume":"10","author":"S Diguistini","year":"2009","unstructured":"Diguistini S, Liao N, Platt D, Robertson G, Seidel M, Chan S, Docking T, Birol I, Holt R, Hirst M, Mardis E, Marra M, Hamelin R, Bohlmann J, Breuil C, Jones S: De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data. Genome Biol. 2009, 10: R94-10.1186\/gb-2009-10-9-r94.","journal-title":"Genome Biol"},{"issue":"6","key":"6110_CR6","doi-asserted-by":"publisher","first-page":"e10922","DOI":"10.1371\/journal.pone.0010922","volume":"5","author":"H Nagarajan","year":"2010","unstructured":"Nagarajan H, Butler J, Klimes A, Qiu Y, Zengler K, Ward J, Young N, Meth B, Palsson B, Lovley D, Barrett C: De Novo assembly of the complete genome of an enhanced electricity-producing variant of Geobacter sulfurreducens using only short reads. PLoS One. 2010, 5 (6): e10922-10.1371\/journal.pone.0010922.","journal-title":"PLoS One"},{"key":"6110_CR7","volume-title":"Bioinformatics and Biomedicine","author":"A Casagrande","year":"2009","unstructured":"Casagrande A, Del FC, Scalabrin S, Policriti A: GAM: Genomic Assemblies Merger: A Graph Based Method to Integrate Different Assemblies. Bioinformatics and Biomedicine. 2009, 10.1109\/BIBM.2009.28"},{"key":"6110_CR8","doi-asserted-by":"publisher","first-page":"64","DOI":"10.1186\/1471-2105-8-64","volume":"8","author":"D Sommer","year":"2007","unstructured":"Sommer D, Delcher A, Salzberg A, Pop M: Minimus: a fast, lightweight genome assembler. BMC Bioinformatics. 2007, 8: 64-10.1186\/1471-2105-8-64.","journal-title":"BMC Bioinformatics"},{"issue":"18","key":"6110_CR9","doi-asserted-by":"publisher","first-page":"i433","DOI":"10.1093\/bioinformatics\/btq366","volume":"26","author":"J Nijkamp","year":"2010","unstructured":"Nijkamp J, Winterbach W, van dBM, Daran J, Reinders M, de Ridder R: Integrating genome assemblies with MAIA. Bioinformatics. 2010, 26 (18): i433-9. 10.1093\/bioinformatics\/btq366.","journal-title":"Bioinformatics"},{"key":"6110_CR10","doi-asserted-by":"publisher","first-page":"42","DOI":"10.1093\/bioinformatics\/btm542","volume":"24","author":"A Zimin","year":"2008","unstructured":"Zimin A, Smith D, Sutton G, Yorke J: Assembly reconciliation. Bioinformatics. 2008, 24: 42-5. 10.1093\/bioinformatics\/btm542.","journal-title":"Bioinformatics"},{"issue":"12","key":"6110_CR11","doi-asserted-by":"publisher","first-page":"2258","DOI":"10.1101\/gr.091777.109","volume":"19","author":"J Argueso","year":"2009","unstructured":"Argueso J, Carazzolle M, Mieczkowski P, Duarte F, Netto O, Missawa S, Galzerani F, Costa G, Vidal R, Noronha M, Dominska M, Andrietta M, Andrietta S, Cunha A, Gomes L, Tavares F, Alcarde A, Dietrich F, McCusker J, Petes T, Pereira G: Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production. Genome Res. 2009, 19 (12): 2258-2270. 10.1101\/gr.091777.109.","journal-title":"Genome Res"},{"issue":"7","key":"6110_CR12","first-page":"1","volume":"14","author":"R Vicedomini","year":"2013","unstructured":"Vicedomini R, Vezzi F, Scalabrin S, Arvestad L, Policriti A: GAM-NGS: genomic assemblies merger for next generation sequencing. BMC Bioinformatics. 2013, 14 (7): 1-18.","journal-title":"BMC Bioinformatics"},{"issue":"2","key":"6110_CR13","doi-asserted-by":"publisher","first-page":"R12","DOI":"10.1186\/gb-2004-5-2-r12","volume":"5","author":"A Kurtz","year":"2004","unstructured":"Kurtz A, Phillippy A, Delcher A, Smoot M, Shumway A, Antonescu C, Salzberg S: Versatile and open software for comparing large genomes. Genome Biology. 2004, 5 (2): R12-10.1186\/gb-2004-5-2-r12.","journal-title":"Genome Biology"},{"key":"6110_CR14","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1093\/bioinformatics\/btr588","volume":"28","author":"G Yao","year":"2011","unstructured":"Yao G, Ye L, Gao H, Minx P, Warren W, Weinstock G: Graph accordance of next-generation sequence assemblies. Bioinformatics. 2011, 28: 13-6.","journal-title":"Bioinformatics"},{"key":"6110_CR15","volume-title":"Bioinformatics","author":"T Magoc","year":"2013","unstructured":"Magoc T, Pabinger S, Canzar S, Liu X, Su Q, Puiu D, Tallon L, Salzberg S: GAGE-B: An Evaluation of Genome Assemblers for Bacterial Organisms. Bioinformatics. 2013"},{"key":"6110_CR16","doi-asserted-by":"publisher","first-page":"82","DOI":"10.1007\/BF02523689","volume":"18","author":"D Karger","year":"1997","unstructured":"Karger D, Motwani R, Ramkumar G: On Approximating the longest path in a graph. Algorithmica. 1997, 18: 82-98. 10.1007\/BF02523689.","journal-title":"Algorithmica"},{"key":"6110_CR17","first-page":"530","volume-title":"Computer Design: VLSI in Computers and Processors, 1998 ICCD '98 Proceedings International Conference on","author":"YC Hsu","year":"1998","unstructured":"Hsu YC, Sun S, Du DC: Finding the longest simple path in cyclic combinational circuits. Computer Design: VLSI in Computers and Processors, 1998 ICCD '98 Proceedings International Conference on. 1998, 530-535."},{"key":"6110_CR18","volume-title":"Random Graphs","author":"B Bollobas","year":"1985","unstructured":"Bollobas B: Random Graphs. 1985, Academic Press"},{"issue":"8","key":"6110_CR19","doi-asserted-by":"publisher","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","volume":"29","author":"A Gurevich","year":"2013","unstructured":"Gurevich A, Saveliev V, Vyahhi N, Tesler G: QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013, 29 (8): 1072-1075. 10.1093\/bioinformatics\/btt086.","journal-title":"Bioinformatics"},{"key":"6110_CR20","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1089\/cmb.2012.0021","volume":"19","author":"A Bankevich","year":"2012","unstructured":"Bankevich A, Nurk S, Antipov D, Gurevich A, Dvorkin M, Kulikov A, Lesin V, Nikolenko S, Pham S, Prjibelski A, Pyshkin A, Sirotkin A, Vyahhi N, Tesler G, Alekseyev M, Pevzner P: SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012, 19: 455-477. 10.1089\/cmb.2012.0021.","journal-title":"J Comput Biol"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-14-S15-S16.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,2]],"date-time":"2021-09-02T01:40:02Z","timestamp":1630546802000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-14-S15-S16"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,10]]},"references-count":20,"journal-issue":{"issue":"S15","published-print":{"date-parts":[[2013,10]]}},"alternative-id":["6110"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-14-s15-s16","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,10]]},"assertion":[{"value":"15 October 2013","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S16"}}