{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T14:47:30Z","timestamp":1740149250124,"version":"3.37.3"},"reference-count":57,"publisher":"Springer Science and Business Media LLC","issue":"3","license":[{"start":{"date-parts":[[2023,5,28]],"date-time":"2023-05-28T00:00:00Z","timestamp":1685232000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2023,5,28]],"date-time":"2023-05-28T00:00:00Z","timestamp":1685232000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"funder":[{"DOI":"10.13039\/100014718","name":"Innovative Research Group Project of the National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62002388"],"award-info":[{"award-number":["62002388"]}],"id":[{"id":"10.13039\/100014718","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004735","name":"Natural Science Foundation of Hunan Province","doi-asserted-by":"publisher","award":["2021JJ40787"],"award-info":[{"award-number":["2021JJ40787"]}],"id":[{"id":"10.13039\/501100004735","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["New Gener. Comput."],"published-print":{"date-parts":[[2023,9]]},"DOI":"10.1007\/s00354-023-00221-6","type":"journal-article","created":{"date-parts":[[2023,5,28]],"date-time":"2023-05-28T12:01:51Z","timestamp":1685275311000},"page":"553-579","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["An Optimized Scaffolding Algorithm for Unbalanced Sequencing"],"prefix":"10.1007","volume":"41","author":[{"given":"Wufei","family":"Zhu","sequence":"first","affiliation":[]},{"given":"Ying","family":"Liu","sequence":"additional","affiliation":[]},{"given":"Ya","family":"Zhao","sequence":"additional","affiliation":[]},{"given":"Xingyu","family":"Liao","sequence":"additional","affiliation":[]},{"given":"Mingxu","family":"Tong","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0061-1317","authenticated-orcid":false,"given":"Xiangyu","family":"Liao","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2023,5,28]]},"reference":[{"key":"221_CR1","doi-asserted-by":"publisher","first-page":"30","DOI":"10.1186\/s13059-020-1935-5","volume":"21","author":"SL Amarasinghe","year":"2020","unstructured":"Amarasinghe, S.L., Su, S., Dong, X., et al.: Opportunities and challenges in long-read sequencing data analysis. Genome Biol. 21, 30 (2020)","journal-title":"Genome Biol."},{"key":"221_CR2","doi-asserted-by":"publisher","first-page":"1348","DOI":"10.1038\/s41587-021-01108-x","volume":"39","author":"Y Wang","year":"2021","unstructured":"Wang, Y., Zhao, Y., Bollas, A., et al.: Nanopore sequencing technology, bioinformatics and applications. Nat. Biotechnol. 39, 1348\u20131365 (2021)","journal-title":"Nat. Biotechnol."},{"key":"221_CR3","doi-asserted-by":"publisher","first-page":"426","DOI":"10.3389\/fgene.2019.00426","volume":"10","author":"T Mantere","year":"2019","unstructured":"Mantere, T., Kersten, S., Hoischen, A.: Long-Read Sequencing Emerging in Medical Genetics. Front. Genet. 10, 426 (2019)","journal-title":"Front. Genet."},{"issue":"24","key":"221_CR4","doi-asserted-by":"publisher","first-page":"2818","DOI":"10.1093\/bioinformatics\/btn548","volume":"24","author":"JR Miller","year":"2008","unstructured":"Miller, J.R., Delcher, A.L., Koren, S., et al.: Aggressive assembly of pyrosequencing reads with mates. Bioinformatics 24(24), 2818\u20132824 (2008)","journal-title":"Bioinformatics"},{"key":"221_CR5","doi-asserted-by":"publisher","DOI":"10.1109\/TCBB.2019.2897558","author":"X Liao","year":"2019","unstructured":"Liao, X., Li, M., Zou, Y., et al.: An efficient trimming algorithm based on multi-feature fusion scoring model for NGS data. IEEE\/ACM Trans. Comput. Biol. Bioinform. (2019). https:\/\/doi.org\/10.1109\/TCBB.2019.2897558","journal-title":"IEEE\/ACM Trans. Comput. Biol. Bioinform."},{"issue":"5","key":"221_CR6","doi-asserted-by":"publisher","first-page":"821","DOI":"10.1101\/gr.074492.107","volume":"18","author":"DR Zerbino","year":"2008","unstructured":"Zerbino, D.R., Birney, E.: Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18(5), 821\u2013829 (2008)","journal-title":"Genome Res."},{"issue":"3","key":"221_CR7","doi-asserted-by":"publisher","first-page":"R42","DOI":"10.1186\/gb-2014-15-3-r42","volume":"15","author":"M Hunt","year":"2014","unstructured":"Hunt, M., Newbold, C., Berriman, M., et al.: A comprehensive evaluation of assembly scaffolding tools. Genome Biol. 15(3), R42 (2014)","journal-title":"Genome Biol."},{"issue":"5","key":"221_CR8","doi-asserted-by":"publisher","first-page":"603","DOI":"10.1145\/585265.585267","volume":"49","author":"DH Huson","year":"2002","unstructured":"Huson, D.H., Reinert, K., Myers, E.W.: The greedy path-merging algorithm for contig scaffolding. J. ACM (JACM) 49(5), 603\u2013615 (2002)","journal-title":"J. ACM (JACM)"},{"key":"221_CR9","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1007\/BF01188580","volume":"13","author":"JD Kececioglu","year":"1995","unstructured":"Kececioglu, J.D., Myers, E.W.: Combinatorial algorithms for DNA sequence assembly. Algorithmica 13, 7\u201315 (1995)","journal-title":"Algorithmica"},{"issue":"23","key":"221_CR10","doi-asserted-by":"publisher","first-page":"3259","DOI":"10.1093\/bioinformatics\/btr562","volume":"27","author":"L Salmela","year":"2011","unstructured":"Salmela, L., M\u00e4kinen, V., V\u00e4lim\u00e4ki, N., et al.: Fast scaffolding with small independent mixed integer programs. Bioinformatics 27(23), 3259\u20133265 (2011)","journal-title":"Bioinformatics"},{"issue":"6","key":"221_CR11","doi-asserted-by":"publisher","first-page":"825","DOI":"10.1093\/bioinformatics\/btu762","volume":"31","author":"J Luo","year":"2014","unstructured":"Luo, J., Wang, J., Zhang, Z., et al.: EPGA: de novo assembly using the distributions of reads and insert size. Bioinformatics 31(6), 825\u2013833 (2014)","journal-title":"Bioinformatics"},{"issue":"24","key":"221_CR12","doi-asserted-by":"publisher","first-page":"3988","DOI":"10.1093\/bioinformatics\/btv487","volume":"31","author":"J Luo","year":"2015","unstructured":"Luo, J., Wang, J., Li, W., et al.: EPGA2: memory-efficient de novo assembler. Bioinformatics 31(24), 3988\u20133990 (2015)","journal-title":"Bioinformatics"},{"issue":"6","key":"221_CR13","doi-asserted-by":"publisher","first-page":"1117","DOI":"10.1101\/gr.089532.108","volume":"19","author":"JT Simpson","year":"2009","unstructured":"Simpson, J.T., Wong, K., Jackman, S.D., et al.: ABySS: a parallel assembler for short read sequence data. Genome Res. 19(6), 1117\u20131123 (2009)","journal-title":"Genome Res."},{"issue":"1","key":"221_CR14","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1186\/2047-217X-1-18","volume":"1","author":"R Luo","year":"2012","unstructured":"Luo, R., Liu, B., Xie, Y., et al.: SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 1(1), 18 (2012)","journal-title":"Gigascience"},{"issue":"5","key":"221_CR15","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., 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."},{"issue":"11","key":"221_CR16","doi-asserted-by":"publisher","first-page":"1420","DOI":"10.1093\/bioinformatics\/bts174","volume":"28","author":"Y Peng","year":"2012","unstructured":"Peng, Y., Leung, H.C.M., Yiu, S.M., et al.: 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":"5","key":"221_CR17","doi-asserted-by":"publisher","first-page":"810","DOI":"10.1101\/gr.7337908","volume":"18","author":"J Butler","year":"2008","unstructured":"Butler, J., MacCallum, I., Kleber, M., et al.: ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res. 18(5), 810\u2013820 (2008)","journal-title":"Genome Res."},{"key":"221_CR18","doi-asserted-by":"publisher","first-page":"1050","DOI":"10.1038\/nmeth.4035","volume":"13","author":"CS Chin","year":"2016","unstructured":"Chin, C.S., Peluso, P., Sedlazeck, F., et al.: Phased diploid genome assembly with single-molecule real-time sequencing. Nat. Methods 13, 1050\u20131054 (2016)","journal-title":"Nat. Methods"},{"key":"221_CR19","doi-asserted-by":"publisher","first-page":"540","DOI":"10.1038\/s41587-019-0072-8","volume":"37","author":"M Kolmogorov","year":"2019","unstructured":"Kolmogorov, M., Yuan, J., Lin, Y., et al.: Assembly of long, error-prone reads using repeat graphs. Nat. Biotechnol. 37, 540\u2013546 (2019)","journal-title":"Nat. Biotechnol."},{"issue":"14","key":"221_CR20","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":"5","key":"221_CR21","doi-asserted-by":"publisher","first-page":"722","DOI":"10.1101\/gr.215087.116","volume":"27","author":"S Koren","year":"2017","unstructured":"Koren, S., Walenz, B.P., Berlin, K., et al.: Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 27(5), 722\u2013736 (2017)","journal-title":"Genome Res."},{"issue":"2","key":"221_CR22","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1038\/s41592-019-0669-3","volume":"17","author":"J Ruan","year":"2020","unstructured":"Ruan, J., Li, H.: Fast and accurate long-read assembly with wtdbg2. Nat. Methods 17(2), 155\u2013158 (2020)","journal-title":"Nat. Methods"},{"key":"221_CR23","doi-asserted-by":"crossref","unstructured":"Deshpande, V., Fung, E.D.K., Pham, S., et al.: Cerulean: A Hybrid Assembly Using High Throughput Short and Long Reads. International Workshop on Algorithms in Bioinformatics, vol. 8126. Springer, Berlin, Heidelberg (2013)","DOI":"10.1007\/978-3-642-40453-5_27"},{"issue":"7","key":"221_CR24","doi-asserted-by":"publisher","first-page":"1009","DOI":"10.1093\/bioinformatics\/btv688","volume":"32","author":"A Dmitry","year":"2016","unstructured":"Dmitry, A., Anton, K., Jeffrey, S., et al.: HYBRIDSPADES: an algorithm for hybrid assembly of short and long reads. Bioinformatics 32(7), 1009\u20131015 (2016)","journal-title":"Bioinformatics"},{"key":"221_CR25","doi-asserted-by":"publisher","first-page":"31900","DOI":"10.1038\/srep31900","volume":"6","author":"C Ye","year":"2016","unstructured":"Ye, C., Hill, C., Wu, S., et al.: DBG2OLC: Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies. Sci. Rep. 6, 31900 (2016)","journal-title":"Sci. Rep."},{"key":"221_CR26","doi-asserted-by":"publisher","first-page":"709","DOI":"10.1056\/NEJMoa1106920","volume":"365","author":"DA Rasko","year":"2011","unstructured":"Rasko, D.A., Webster, D.R., Sahl, J.W., et al.: Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany. N. Engl. J. Med. 365, 709\u2013717 (2011)","journal-title":"N. Engl. J. Med."},{"key":"221_CR27","doi-asserted-by":"publisher","first-page":"693","DOI":"10.1038\/nbt.2280","volume":"30","author":"S Koren","year":"2012","unstructured":"Koren, S., Schatz, M.C., Walenz, B.P., et al.: Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat. Biotechnol. 30, 693\u2013700 (2012)","journal-title":"Nat. Biotechnol."},{"key":"221_CR28","doi-asserted-by":"publisher","first-page":"1750","DOI":"10.1101\/gr.191395.115","volume":"25","author":"S Goodwin","year":"2015","unstructured":"Goodwin, S., Gurtowski, J., Ethe-Sayers, S., et al.: Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome. Genome Res. 25, 1750\u20131756 (2015)","journal-title":"Genome Res."},{"key":"221_CR29","doi-asserted-by":"publisher","first-page":"623","DOI":"10.1038\/nbt.3238","volume":"33","author":"K Berlin","year":"2015","unstructured":"Berlin, K., Koren, S., Chin, C.S., et al.: Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. Nat. Biotechnol. 33, 623\u2013630 (2015)","journal-title":"Nat. Biotechnol."},{"issue":"4","key":"221_CR30","doi-asserted-by":"publisher","first-page":"578","DOI":"10.1093\/bioinformatics\/btq683","volume":"27","author":"M Boetzer","year":"2010","unstructured":"Boetzer, M., Henkel, C.V., Jansen, H.J., et al.: Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 27(4), 578\u2013579 (2010)","journal-title":"Bioinformatics"},{"issue":"2","key":"221_CR31","doi-asserted-by":"publisher","first-page":"169","DOI":"10.1093\/bioinformatics\/btw597","volume":"33","author":"J Luo","year":"2017","unstructured":"Luo, J., Wang, J., Zhang, Z., et al.: BOSS: a novel scaffolding algorithm based on an optimized scaffold graph. Bioinformatics 33(2), 169\u2013176 (2017)","journal-title":"Bioinformatics"},{"issue":"16","key":"221_CR32","doi-asserted-by":"publisher","first-page":"2632","DOI":"10.1093\/bioinformatics\/btv211","volume":"31","author":"I Mandric","year":"2015","unstructured":"Mandric, I., Zelikovsky, A.: ScaffMatch: scaffolding algorithm based on maximum weight matching. Bioinformatics 31(16), 2632\u20132638 (2015)","journal-title":"Bioinformatics"},{"issue":"7","key":"221_CR33","doi-asserted-by":"publisher","first-page":"1142","DOI":"10.1093\/bioinformatics\/bty773","volume":"35","author":"M Li","year":"2019","unstructured":"Li, M., Tang, L., Wu, F.X., Pan, Y., Wang, J.: SCOP: a novel scaffolding algorithm based on contig classification and optimization. Bioinformatics 35(7), 1142\u20131150 (2019)","journal-title":"Bioinformatics"},{"issue":"1","key":"221_CR34","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1101\/gr.1536204","volume":"14","author":"M Pop","year":"2004","unstructured":"Pop, M., Kosack, D.S., Salzberg, S.L.: Hierarchical scaffolding with Bambus. Genome Res. 14(1), 149\u2013159 (2004)","journal-title":"Genome Res."},{"issue":"1","key":"221_CR35","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1186\/1471-2105-15-281","volume":"15","author":"K Sahlin","year":"2014","unstructured":"Sahlin, K., Vezzi, F., Nystedt, B., et al.: BESST-efficient scaffolding of large fragmented assemblies. BMC Bioinform. 15(1), 281 (2014)","journal-title":"BMC Bioinform."},{"issue":"1","key":"221_CR36","doi-asserted-by":"publisher","first-page":"345","DOI":"10.1186\/1471-2105-11-345","volume":"11","author":"A Dayarian","year":"2010","unstructured":"Dayarian, A., Michael, T.P., Sengupta, A.M.: SOPRA: Scaffolding algorithm for paired reads via statistical optimization. BMC Bioinform. 11(1), 345 (2010)","journal-title":"BMC Bioinform."},{"issue":"5950","key":"221_CR37","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1126\/science.1181369","volume":"326","author":"E Lieberman-Aiden","year":"2009","unstructured":"Lieberman-Aiden, E., van Berkum, N.L., Williams, L., et al.: Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326(5950), 289\u2013293 (2009)","journal-title":"Science"},{"issue":"12","key":"221_CR38","doi-asserted-by":"publisher","first-page":"1119","DOI":"10.1038\/nbt.2727","volume":"31","author":"JN Burton","year":"2013","unstructured":"Burton, J.N., Adey, A., Patwardhan, R.P., et al.: Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nat. Biotechnol. 31(12), 1119\u20131125 (2013)","journal-title":"Nat. Biotechnol."},{"issue":"3","key":"221_CR39","doi-asserted-by":"publisher","first-page":"342","DOI":"10.1101\/gr.193474.115","volume":"26","author":"NH Putnam","year":"2016","unstructured":"Putnam, N.H., O\u2019Connell, B.L., Stites, J.C., et al.: Chromosome-scale shotgun assembly using an in vitro method for long-range linkage. Genome Res. 26(3), 342\u2013350 (2016)","journal-title":"Genome Res."},{"issue":"6333","key":"221_CR40","doi-asserted-by":"publisher","first-page":"92","DOI":"10.1126\/science.aal3327","volume":"356","author":"O Dudchenko","year":"2017","unstructured":"Dudchenko, O., Batra, S.S., Omer, A.D., et al.: De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science 356(6333), 92\u201395 (2017)","journal-title":"Science"},{"issue":"8","key":"221_CR41","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1007273","volume":"15","author":"J Ghurye","year":"2019","unstructured":"Ghurye, J., Rhie, A., Walenz, B.P., et al.: Integrating Hi-C links with assembly graphs for chromosome-scale assembly. PLoS Comput. Biol. 15(8), e1007273 (2019)","journal-title":"PLoS Comput. Biol."},{"key":"221_CR42","doi-asserted-by":"publisher","first-page":"784","DOI":"10.1186\/s12864-017-4162-z","volume":"18","author":"N Kono","year":"2017","unstructured":"Kono, N., Tomita, M., Arakawa, K.: eRP arrangement: a strategy for assembled genomic contig rearrangement based on replication profiling in bacteria. BMC Genom. 18, 784 (2017)","journal-title":"BMC Genom."},{"issue":"8","key":"221_CR43","doi-asserted-by":"publisher","first-page":"833","DOI":"10.1038\/s41477-019-0487-8","volume":"5","author":"X Zhang","year":"2019","unstructured":"Zhang, X., Zhang, S., Zhao, Q., et al.: Assembly of allele-aware, chromosomal-scale autopolyploid genomes based on Hi-C data. Nat Plants 5(8), 833\u2013845 (2019)","journal-title":"Nat Plants"},{"issue":"1","key":"221_CR44","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1186\/1471-2105-15-211","volume":"15","author":"M Boetzer","year":"2014","unstructured":"Boetzer, M., Pirovano, W.: SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information. BMC Bioinform. 15(1), 211 (2014)","journal-title":"BMC Bioinform."},{"key":"221_CR45","doi-asserted-by":"publisher","first-page":"102","DOI":"10.1186\/s13059-016-0951-y","volume":"17","author":"S Gao","year":"2016","unstructured":"Gao, S., Bertrand, D., Chia, B.K.H., et al.: OPERA-LG: efficient and exact scaffolding of large, repeat-rich eukaryotic genomes with performance guarantees. Genome Biol. 17, 102 (2016)","journal-title":"Genome Biol."},{"key":"221_CR46","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1186\/s13742-015-0076-3","volume":"4","author":"RL Warren","year":"2015","unstructured":"Warren, R.L., Yang, C., Vandervalk, B.P., et al.: LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads. GigaSci 4, 35 (2015)","journal-title":"GigaSci"},{"issue":"1","key":"221_CR47","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1007\/s12532-009-0002-8","volume":"1","author":"V Kolmogorov","year":"2009","unstructured":"Kolmogorov, V.: Blossom V: a new implementation of a minimum cost perfect matching algorithm. Math. Program. 1(1), 43\u201367 (2009)","journal-title":"Math. Program."},{"issue":"4","key":"221_CR48","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","volume":"9","author":"B Langmead","year":"2012","unstructured":"Langmead, B., Salzberg, S.L.: Fast gapped-read alignment with Bowtie 2. Nat. Methods 9(4), 357 (2012)","journal-title":"Nat. Methods"},{"issue":"14","key":"221_CR49","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","volume":"25","author":"H Li","year":"2009","unstructured":"Li, H., Durbin, R.: Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25(14), 1754\u20131760 (2009)","journal-title":"Bioinformatics"},{"key":"221_CR50","doi-asserted-by":"publisher","first-page":"494","DOI":"10.1186\/s12864-016-2821-0","volume":"17","author":"K Kojima","year":"2016","unstructured":"Kojima, K., Kawai, Y., Nariai, N., et al.: Short tandem repeat number estimation from paired-end reads for multiple individuals by considering coalescent tree. BMC Genom. 17, 494 (2016)","journal-title":"BMC Genom."},{"key":"221_CR51","doi-asserted-by":"publisher","DOI":"10.1109\/TCBB.2018.2861380","author":"X Liao","year":"2018","unstructured":"Liao, X., Li, M., Zou, Y., et al.: Improving de novo assembly based on read classification. IEEE\/ACM Trans. Comput. Biol. Bioinform. (2018). https:\/\/doi.org\/10.1109\/TCBB.2018.2861380","journal-title":"IEEE\/ACM Trans. Comput. Biol. Bioinform."},{"key":"221_CR52","doi-asserted-by":"publisher","DOI":"10.1109\/TCBB.2018.2876855","author":"B Wu","year":"2018","unstructured":"Wu, B., Li, M., Liao, X., et al.: MEC: Misassembly Error Correction in contigs based on distribution of paired-end reads and statistics of GC-contents. IEEE\/ACM Trans. Comput. Biol. Bioinform. (2018). https:\/\/doi.org\/10.1109\/TCBB.2018.2876855","journal-title":"IEEE\/ACM Trans. Comput. Biol. Bioinform."},{"issue":"8","key":"221_CR53","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., et al.: QUAST: quality assessment tool for genome assemblies. Bioinformatics 29(8), 1072\u20131075 (2013)","journal-title":"Bioinformatics"},{"issue":"4","key":"221_CR54","doi-asserted-by":"publisher","first-page":"916","DOI":"10.1109\/TCBB.2016.2550433","volume":"14","author":"M Li","year":"2017","unstructured":"Li, M., Liao, Z., He, Y., et al.: ISEA: iterative seed-extension algorithm for de novo assembly using paired-end information and insert size distribution. IEEE\/ACM Trans. Comput. Biol. Bioinform. 14(4), 916\u2013925 (2017)","journal-title":"IEEE\/ACM Trans. Comput. Biol. Bioinform."},{"key":"221_CR55","doi-asserted-by":"publisher","DOI":"10.1109\/TCBB.2018.2789909","author":"J Luo","year":"2018","unstructured":"Luo, J., Wang, J., Shang, J., et al.: GapReduce: a gap filling algorithm based on partitioned read sets. IEEE\/ACM Trans. Comput. Biol. Bioinform. (2018). https:\/\/doi.org\/10.1109\/TCBB.2018.2789909","journal-title":"IEEE\/ACM Trans. Comput. Biol. Bioinform."},{"key":"221_CR56","doi-asserted-by":"publisher","first-page":"178","DOI":"10.1016\/j.compbiolchem.2017.03.012","volume":"69","author":"M Li","year":"2017","unstructured":"Li, M., Wu, B., Yan, X., et al.: PECC: correcting contigs based on paired-end read distribution. Comput. Biol. Chem. 69, 178\u2013184 (2017)","journal-title":"Comput. Biol. Chem."},{"issue":"1","key":"221_CR57","doi-asserted-by":"publisher","first-page":"44","DOI":"10.3390\/genes10010044","volume":"10","author":"W Zhang","year":"2019","unstructured":"Zhang, W., Huang, N., Zheng, J., et al.: A Sequence-Based Novel Approach for Quality Evaluation of Third-Generation Sequencing Reads. Genes 10(1), 44 (2019)","journal-title":"Genes"}],"container-title":["New Generation Computing"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00354-023-00221-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s00354-023-00221-6\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00354-023-00221-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,16]],"date-time":"2023-09-16T10:08:00Z","timestamp":1694858880000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s00354-023-00221-6"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,5,28]]},"references-count":57,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2023,9]]}},"alternative-id":["221"],"URL":"https:\/\/doi.org\/10.1007\/s00354-023-00221-6","relation":{},"ISSN":["0288-3635","1882-7055"],"issn-type":[{"type":"print","value":"0288-3635"},{"type":"electronic","value":"1882-7055"}],"subject":[],"published":{"date-parts":[[2023,5,28]]},"assertion":[{"value":"3 October 2022","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"4 May 2023","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"28 May 2023","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of interest"}}]}}