{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T00:41:19Z","timestamp":1790728879777,"version":"4.1.0"},"reference-count":50,"publisher":"Springer Science and Business Media LLC","issue":"S4","license":[{"start":{"date-parts":[[2019,4,1]],"date-time":"2019-04-01T00:00:00Z","timestamp":1554076800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2019,4]]},"DOI":"10.1186\/s12859-019-2691-y","type":"journal-article","created":{"date-parts":[[2019,4,18]],"date-time":"2019-04-18T09:07:39Z","timestamp":1555578459000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":26,"title":["GenHap: a novel computational method based on genetic algorithms for haplotype assembly"],"prefix":"10.1186","volume":"20","author":[{"given":"Andrea","family":"Tangherloni","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simone","family":"Spolaor","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leonardo","family":"Rundo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marco S.","family":"Nobile","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paolo","family":"Cazzaniga","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Giancarlo","family":"Mauri","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pietro","family":"Li\u00f2","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ivan","family":"Merelli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniela","family":"Besozzi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2019,4,18]]},"reference":[{"issue":"10","key":"2691_CR1","doi-asserted-by":"publisher","first-page":"e254","DOI":"10.1371\/journal.pbio.0050254","volume":"5","author":"Samuel Levy","year":"2007","unstructured":"Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, Walenz BP, Axelrod N, Huang J, Kirkness EF, Denisov G, et al.The diploid genome sequence of an individual human. PLoS Biol. 2007; 5(10):254. \n                    https:\/\/doi.org\/10.1371\/journal.pbio.0050254\n                    \n                  .","journal-title":"PLoS Biology"},{"issue":"2","key":"2691_CR2","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1038\/nrg1521","volume":"6","author":"Joel N. Hirschhorn","year":"2005","unstructured":"Hirschhorn JN, Daly MJ. Genome-wide association studies for common diseases and complex traits. Nat Rev Genet. 2005; 6(2):95. \n                    https:\/\/doi.org\/10.1038\/nrg1521\n                    \n                  .","journal-title":"Nature Reviews Genetics"},{"issue":"6","key":"2691_CR3","doi-asserted-by":"publisher","first-page":"344","DOI":"10.1038\/nrg3903","volume":"16","author":"Matthew W. Snyder","year":"2015","unstructured":"Snyder M, Adey A, Kitzman JO, Shendure J. Haplotype-resolved genome sequencing: experimental methods and applications. Nat Rev Genet. 2015; 16(6):344\u201358. \n                    https:\/\/doi.org\/10.1038\/nrg3903\n                    \n                  .","journal-title":"Nature Reviews Genetics"},{"issue":"3","key":"2691_CR4","doi-asserted-by":"publisher","first-page":"261","DOI":"10.1038\/nbt.2833","volume":"32","author":"V Kuleshov","year":"2014","unstructured":"Kuleshov V, Xie D, Chen R, Pushkarev D, Ma Z, Blauwkamp T, Kertesz M, Snyder M. Whole-genome haplotyping using long reads and statistical methods. Nat Biotech. 2014; 32(3):261\u20136.","journal-title":"Nat Biotech"},{"issue":"6","key":"2691_CR5","doi-asserted-by":"publisher","first-page":"498","DOI":"10.1089\/cmb.2014.0157","volume":"22","author":"Murray Patterson","year":"2015","unstructured":"Patterson M, Marschall T, Pisanti N, Van Iersel L, Stougie L, Klau GW, Sch\u00f6nhuth A. WhatsHap: weighted haplotype assembly for future-generation sequencing reads. J Comput Biol. 2015; 22(6):498\u2013509. \n                    https:\/\/doi.org\/10.1089\/cmb.2014.0157\n                    \n                  .","journal-title":"Journal of Computational Biology"},{"issue":"6","key":"2691_CR6","doi-asserted-by":"publisher","first-page":"1386","DOI":"10.1086\/344780","volume":"71","author":"Kui Zhang","year":"2002","unstructured":"Zhang K, Calabrese P, Nordborg M, Sun F. Haplotype block structure and its applications to association studies: power and study designs. Am J Hum Genet. 2002; 71(6):1386\u201394. \n                    https:\/\/doi.org\/10.1086\/344780\n                    \n                  .","journal-title":"The American Journal of Human Genetics"},{"issue":"2","key":"2691_CR7","doi-asserted-by":"publisher","first-page":"229","DOI":"10.1038\/ng1001-229","volume":"29","author":"Mark J. Daly","year":"2001","unstructured":"Daly MJ, Rioux JD, Schaffner SF, Hudson TJ, Lander ES. High-resolution haplotype structure in the human genome. Nat Genet. 2001; 29(2):229. \n                    https:\/\/doi.org\/10.1038\/ng1001-229\n                    \n                  .","journal-title":"Nature Genetics"},{"issue":"5","key":"2691_CR8","doi-asserted-by":"publisher","first-page":"278","DOI":"10.1016\/j.gpb.2015.08.002","volume":"13","author":"Anthony Rhoads","year":"2015","unstructured":"Rhoads A, Au KF. PacBio sequencing and its applications. Genom Proteom Bioinf. 2015; 13(5):278\u201389. \n                    https:\/\/doi.org\/10.1016\/j.gpb.2015.08.002\n                    \n                  .","journal-title":"Genomics, Proteomics & Bioinformatics"},{"key":"2691_CR9","doi-asserted-by":"crossref","unstructured":"Roberts RJ, Carneiro MO, Schatz MC. The advantages of SMRT sequencing. Genome Biol. 2013; 14(6):405. \n                    https:\/\/doi.org\/10.1186\/gb-2013-14-6-405\n                    \n                  .","DOI":"10.1186\/gb-2013-14-6-405"},{"issue":"4","key":"2691_CR10","doi-asserted-by":"publisher","first-page":"351","DOI":"10.1038\/nmeth.3290","volume":"12","author":"Miten Jain","year":"2015","unstructured":"Jain M, Fiddes IT, Miga KH, Olsen HE, Paten B, Akeson M. Improved data analysis for the MinION nanopore sequencer. Nat Methods. 2015; 12(4):351. \n                    https:\/\/doi.org\/10.1038\/nmeth.3290\n                    \n                  .","journal-title":"Nature Methods"},{"issue":"12","key":"2691_CR11","doi-asserted-by":"publisher","first-page":"1005","DOI":"10.1038\/nmeth.1270","volume":"5","author":"Michael A Quail","year":"2008","unstructured":"Quail MA, Kozarewa I, Smith F, Scally A, Stephens PJ, Durbin R, Swerdlow H, Turner DJ. A large genome center\u2019s improvements to the Illumina sequencing system. Nat Methods. 2008; 5(12):1005. \n                    https:\/\/doi.org\/10.1038\/nmeth.1270\n                    \n                  .","journal-title":"Nature Methods"},{"issue":"10","key":"2691_CR12","doi-asserted-by":"publisher","first-page":"2456","DOI":"10.1093\/bioinformatics\/bti352","volume":"21","author":"R.-S. Wang","year":"2005","unstructured":"Wang RS, Wu LY, Li ZP, Zhang XS. Haplotype reconstruction from SNP fragments by minimum error correction. Bioinformatics. 2005; 21(10):2456\u201362. \n                    https:\/\/doi.org\/10.1093\/bioinformatics\/bti352\n                    \n                  .","journal-title":"Bioinformatics"},{"issue":"1","key":"2691_CR13","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1093\/bib\/3.1.23","volume":"3","author":"R. Lippert","year":"2002","unstructured":"Lippert R, Schwartz R, Lancia G, Istrail S. Algorithmic strategies for the single nucleotide polymorphism haplotype assembly problem. Brief Bioinform. 2002; 3(1):23\u201331. \n                    https:\/\/doi.org\/10.1093\/bib\/3.1.23\n                    \n                  .","journal-title":"Briefings in Bioinformatics"},{"issue":"3","key":"2691_CR14","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1287\/ijoc.1040.0073","volume":"16","author":"Harvey J. Greenberg","year":"2004","unstructured":"Greenberg HJ, Hart WE, Lancia G. Opportunities for combinatorial optimization in computational biology. INFORMS J Comput. 2004; 16(3):211\u201331. \n                    https:\/\/doi.org\/10.1287\/ijoc.1040.0073\n                    \n                  .","journal-title":"INFORMS Journal on Computing"},{"key":"2691_CR15","doi-asserted-by":"crossref","unstructured":"Duitama J, Huebsch T, McEwen G, Suk EK, Hoehe MR. ReFHap: a reliable and fast algorithm for single individual haplotyping. In: Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology. ACM: 2010. p. 160\u20139. \n                    https:\/\/doi.org\/10.1145\/1854776.1854802\n                    \n                  .","DOI":"10.1145\/1854776.1854802"},{"issue":"17","key":"2691_CR16","doi-asserted-by":"publisher","first-page":"i379","DOI":"10.1093\/bioinformatics\/btu484","volume":"30","author":"V. Kuleshov","year":"2014","unstructured":"Kuleshov V. Probabilistic single-individual haplotyping. Bioinformatics. 2014; 30(17):379\u201385. \n                    https:\/\/doi.org\/10.1093\/bioinformatics\/btu484\n                    \n                  .","journal-title":"Bioinformatics"},{"issue":"5","key":"2691_CR17","doi-asserted-by":"publisher","first-page":"922","DOI":"10.1016\/j.jbi.2012.03.004","volume":"45","author":"Tai-Chun Wang","year":"2012","unstructured":"Wang T-C, Taheri J, Zomaya AY. Using genetic algorithm in reconstructing single individual haplotype with minimum error correction. J Biomed Inform. 2012; 45(5):922\u201330. \n                    https:\/\/doi.org\/10.1016\/j.jbi.2012.03.004\n                    \n                  .","journal-title":"Journal of Biomedical Informatics"},{"issue":"11","key":"2691_CR18","doi-asserted-by":"publisher","first-page":"1801","DOI":"10.1093\/bioinformatics\/bty012","volume":"34","author":"Joong Chae Na","year":"2018","unstructured":"Na JC, Lee J-C, Rhee J-K, Shin S-Y. PEATH: Single individual haplotyping by a probabilistic evolutionary algorithm with toggling. Bioinformatics. 2018:bty012. \n                    https:\/\/doi.org\/10.1093\/bioinformatics\/bty012\n                    \n                  .","journal-title":"Bioinformatics"},{"issue":"16","key":"2691_CR19","doi-asserted-by":"publisher","first-page":"1938","DOI":"10.1093\/bioinformatics\/btt349","volume":"29","author":"Zhi-Zhong Chen","year":"2013","unstructured":"Chen ZZ, Deng F, Wang L. Exact algorithms for haplotype assembly from whole-genome sequence data. Bioinformatics. 2013; 29(16):1938\u201345. \n                    https:\/\/doi.org\/10.1093\/bioinformatics\/btt349\n                    \n                  .","journal-title":"Bioinformatics"},{"issue":"12","key":"2691_CR20","doi-asserted-by":"publisher","first-page":"i183","DOI":"10.1093\/bioinformatics\/btq215","volume":"26","author":"D. He","year":"2010","unstructured":"He D, Choi A, Pipatsrisawat K, Darwiche A, Eskin E. Optimal algorithms for haplotype assembly from whole-genome sequence data. Bioinformatics. 2010; 26(12):183\u201390. \n                    https:\/\/doi.org\/10.1093\/bioinformatics\/btq215\n                    \n                  .","journal-title":"Bioinformatics"},{"key":"2691_CR21","series-title":"Lecture Notes in Computer Science","volume-title":"Combinatorial Pattern Matching","year":"2015","unstructured":"Bonizzoni P, Dondi R, Klau GW, Pirola Y, Pisanti N, Zaccaria S. On the fixed parameter tractability and approximability of the minimum error correction problem. In: Proceedings of the Annual Symposium on Combinatorial Pattern Matching (CPM). LNCS. Springer: 2015. p. 100\u201313. \n                    https:\/\/doi.org\/10.1007\/978-3-319-19929-0\n                    \n                  ."},{"key":"2691_CR22","doi-asserted-by":"crossref","unstructured":"Bracciali A, Aldinucci M, Patterson M, Marschall T, Pisanti N, Merelli I, Torquati M. pWhatsHap: efficient haplotyping for future generation sequencing. BMC Bioinform. 2016; 17(Suppl 11):342. \n                    https:\/\/doi.org\/10.1186\/s12859-016-1170-y\n                    \n                  .","DOI":"10.1186\/s12859-016-1170-y"},{"issue":"11","key":"2691_CR23","doi-asserted-by":"publisher","first-page":"1610","DOI":"10.1093\/bioinformatics\/btv495","volume":"32","author":"Yuri Pirola","year":"2015","unstructured":"Pirola Y, Zaccaria S, Dondi R, Klau GW, Pisanti N, Bonizzoni P. HapCol: accurate and memory-efficient haplotype assembly from long reads. Bioinformatics. 2015; 32(11):1610\u20137. \n                    https:\/\/doi.org\/10.1093\/bioinformatics\/btv495\n                    \n                  .","journal-title":"Bioinformatics"},{"issue":"8","key":"2691_CR24","doi-asserted-by":"publisher","first-page":"912","DOI":"10.1038\/ng.3036","volume":"46","author":"Andy Rimmer","year":"2014","unstructured":"Rimmer A, Phan H, Mathieson I, Iqbal Z, Twigg SRF, Wilkie AOM, McVean G, Lunter G, Consortium W, et al.Integrating mapping-, assembly-and haplotype-based approaches for calling variants in clinical sequencing applications. Nat Genet. 2014; 46(8):912. \n                    https:\/\/doi.org\/10.1038\/ng.3036\n                    \n                  .","journal-title":"Nature Genetics"},{"key":"2691_CR25","volume-title":"Genetic Algorithms in Search, Optimization, and Machine Learning. 1st ed","author":"DE Golberg","year":"1989","unstructured":"Golberg DE. Genetic Algorithms in Search, Optimization, and Machine Learning. 1st ed. Boston: Addison-Wesley Longman Publishing Co., Inc.; 1989."},{"key":"2691_CR26","volume-title":"Proceedings of the First International Conference on Genetic Algorithms and Their Applications","author":"JE Baker","year":"1985","unstructured":"Baker JE. Adaptive selection methods for genetic algorithms. In: Proceedings of the First International Conference on Genetic Algorithms and Their Applications. Hillsdale: L. Erlbaum Associates Inc.: 1985. p. 101\u201311."},{"issue":"3","key":"2691_CR27","first-page":"193","volume":"9","author":"BL Miller","year":"1995","unstructured":"Miller BL, Goldberg DE. Genetic algorithms, tournament selection, and the effects of noise. Complex Syst. 1995; 9(3):193\u2013212.","journal-title":"Complex Syst"},{"issue":"104","key":"2691_CR28","doi-asserted-by":"publisher","first-page":"20141335","DOI":"10.1098\/rsif.2014.1335","volume":"12","author":"D. Maisto","year":"2015","unstructured":"Maisto D, Donnarumma F, Pezzulo G. Divide et impera: subgoaling reduces the complexity of probabilistic inference and problem solving. J R Soc Interface. 2015; 12(104):20141335. \n                    https:\/\/doi.org\/10.1098\/rsif.2014.1335\n                    \n                  .","journal-title":"Journal of The Royal Society Interface"},{"key":"2691_CR29","doi-asserted-by":"crossref","unstructured":"Tangherloni A, Rundo L, Spolaor S, Cazzaniga P, Nobile MS. GPU-powered multi-swarm parameter estimation of biological systems: A master-slave approach. In: Proceedings of the 26th Euromicro International Conference on Parallel, Distributed and Network-based Processing (PDP). IEEE: 2018. p. 698\u2013705. \n                    https:\/\/doi.org\/10.1109\/PDP2018.2018.00115\n                    \n                  .","DOI":"10.1109\/PDP2018.2018.00115"},{"key":"2691_CR30","first-page":"650","volume-title":"Lecture Notes in Computer Science","author":"Andrea Tangherloni","year":"2018","unstructured":"Tangherloni A, Rundo L, Spolaor S, Nobile MS, Merelli I, Besozzi D, Mauri G, Cazzaniga P, Li\u00f2 P. High performance computing for haplotyping: models and platforms. In: Proceedings of Euro-Par 2018 (Parallel Processing Workshops). LNCS. Springer: 2018. p. 650\u2013661. \n                    https:\/\/doi.org\/10.1007\/978-3-030-10549-5_51\n                    \n                  ."},{"issue":"1","key":"2691_CR31","doi-asserted-by":"publisher","first-page":"375","DOI":"10.1186\/1471-2164-13-375","volume":"13","author":"Mauricio O Carneiro","year":"2012","unstructured":"Carneiro MO, Russ C, Ross MG, Gabriel SB, Nusbaum C, DePristo MA. Pacific Biosciences sequencing technology for genotyping and variation discovery in human data. BMC Genomics. 2012; 13(1):375. \n                    https:\/\/doi.org\/10.1186\/1471-2164-13-375\n                    \n                  .","journal-title":"BMC Genomics"},{"issue":"1","key":"2691_CR32","doi-asserted-by":"publisher","first-page":"74","DOI":"10.1186\/1471-2164-13-74","volume":"13","author":"Kerensa E McElroy","year":"2012","unstructured":"McElroy KE, Luciani F, Thomas T. GemSIM: general, error-model based simulator of next-generation sequencing data. BMC Genomics. 2012; 13(1):74. \n                    https:\/\/doi.org\/10.1186\/1471-2164-13-74\n                    \n                  .","journal-title":"BMC Genomics"},{"issue":"6","key":"2691_CR33","doi-asserted-by":"publisher","first-page":"1767","DOI":"10.1093\/nar\/gkp1137","volume":"38","author":"Peter J. A. Cock","year":"2009","unstructured":"Cock PJA, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa\/Illumina FASTQ variants. Nucleic Acids Res. 2009; 38(6):1767\u201371. \n                    https:\/\/doi.org\/10.1093\/nar\/gkp1137\n                    \n                  .","journal-title":"Nucleic Acids Research"},{"key":"2691_CR34","doi-asserted-by":"crossref","unstructured":"Casper J, Zweig AS, Villarreal C, Tyner C, Speir ML, Rosenbloom KR, Raney BJ, Lee CM, Lee BT, Karolchik D, et al.The UCSC Genome Browser database: 2018 update. Nucleic Acids Res. 2017; 46(D1):762\u20139. \n                    https:\/\/doi.org\/10.1093\/nar\/gkx1020\n                    \n                  .","DOI":"10.1093\/nar\/gkx1020"},{"issue":"16","key":"2691_CR35","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H. Li","year":"2009","unstructured":"Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The sequence alignment\/map format and SAMtools. Bioinformatics. 2009; 25(16):2078\u20139. \n                    https:\/\/doi.org\/10.1093\/bioinformatics\/btp352\n                    \n                  .","journal-title":"Bioinformatics"},{"issue":"15","key":"2691_CR36","doi-asserted-by":"publisher","first-page":"2156","DOI":"10.1093\/bioinformatics\/btr330","volume":"27","author":"P. Danecek","year":"2011","unstructured":"Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, et al.The variant call format and VCFtools. Bioinformatics. 2011; 27(15):2156\u20138. \n                    https:\/\/doi.org\/10.1093\/bioinformatics\/btr330\n                    \n                  .","journal-title":"Bioinformatics"},{"issue":"9","key":"2691_CR37","doi-asserted-by":"publisher","first-page":"481","DOI":"10.1016\/S0168-9525(01)02409-X","volume":"17","author":"Michael W Nachman","year":"2001","unstructured":"Nachman MW. Single nucleotide polymorphisms and recombination rate in humans. Trends Genet. 2001; 17(9):481\u20135. \n                    https:\/\/doi.org\/10.1016\/S0168-9525(01)02409-X\n                    \n                  .","journal-title":"Trends in Genetics"},{"issue":"5576","key":"2691_CR38","doi-asserted-by":"publisher","first-page":"2225","DOI":"10.1126\/science.1069424","volume":"296","author":"S. B. Gabriel","year":"2002","unstructured":"Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J, Blumenstiel B, Higgins J, DeFelice M, Lochner A, Faggart M, et al.The structure of haplotype blocks in the human genome. Science. 2002; 296(5576):2225\u20139. \n                    https:\/\/doi.org\/10.1126\/science.1069424\n                    \n                  .","journal-title":"Science"},{"key":"2691_CR39","doi-asserted-by":"crossref","unstructured":"Beretta S, Patterson M, Zaccaria S, Della Vedova G, Bonizzoni P. HapCHAT: Adaptive haplotype assembly for efficiently leveraging high coverage in long reads. BMC Bioinform. 2018. \n                    https:\/\/doi.org\/10.1186\/s12859-018-2253-8\n                    \n                  .","DOI":"10.1186\/s12859-018-2253-8"},{"issue":"3","key":"2691_CR40","doi-asserted-by":"publisher","first-page":"246","DOI":"10.1038\/nbt.2835","volume":"32","author":"Justin M Zook","year":"2014","unstructured":"Zook JM, Chapman B, Wang J, Mittelman D, Hofmann O, Hide W, Salit M. Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls. Nat Biotechnol. 2014; 32(3):246\u201351. \n                    https:\/\/doi.org\/10.1038\/nbt.2835\n                    \n                  .","journal-title":"Nature Biotechnology"},{"key":"2691_CR41","unstructured":"Data Release: \u223c54\u00d7 Long-Read Coverage for PacBio-only De Novo Human Genome Assembly. \n                    https:\/\/www.pacb.com\/blog\/data-release-54x-long-read-coverage-for\/\n                    \n                  . Accessed 23 Feb 2019."},{"issue":"7","key":"2691_CR42","doi-asserted-by":"publisher","first-page":"659","DOI":"10.1002\/gepi.20185","volume":"31","author":"Aida M. Andr\u00e9s","year":"2007","unstructured":"Andr\u00e9s AM, Clark AG, Shimmin L, Boerwinkle E, Sing CF, Hixson JE. Understanding the accuracy of statistical haplotype inference with sequence data of known phase. Genet Epidemiol. 2007; 31(7):659\u201371. \n                    https:\/\/doi.org\/10.1002\/gepi.20185\n                    \n                  .","journal-title":"Genetic Epidemiology"},{"key":"2691_CR43","doi-asserted-by":"crossref","unstructured":"Jain M, Olsen HE, Paten B, Akeson M. The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community. Genome Biol. 2016; 17(1):239. \n                    https:\/\/doi.org\/10.1186\/s13059-016-1103-0\n                    \n                  .","DOI":"10.1186\/s13059-016-1103-0"},{"issue":"2","key":"2691_CR44","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1038\/nrg3642","volume":"15","author":"David Sims","year":"2014","unstructured":"Sims D, Sudbery I, Ilott NE, Heger A, Ponting CP. Sequencing depth and coverage: key considerations in genomic analyses. Nat Rev Genet. 2014; 15(2):121. \n                    https:\/\/doi.org\/10.1038\/nrg3642\n                    \n                  .","journal-title":"Nature Reviews Genetics"},{"issue":"17","key":"2691_CR45","doi-asserted-by":"publisher","first-page":"i559","DOI":"10.1093\/bioinformatics\/btw453","volume":"32","author":"Shay Ben-Elazar","year":"2016","unstructured":"Ben-Elazar S, Chor B, Yakhini Z. Extending partial haplotypes to full genome haplotypes using chromosome conformation capture data. Bioinformatics. 2016; 32(17):559\u201366. \n                    https:\/\/doi.org\/10.1093\/bioinformatics\/btw453\n                    \n                  .","journal-title":"Bioinformatics"},{"issue":"13","key":"2691_CR46","doi-asserted-by":"publisher","first-page":"i352","DOI":"10.1093\/bioinformatics\/btt213","volume":"29","author":"Derek Aguiar","year":"2013","unstructured":"Aguiar D, Istrail S. Haplotype assembly in polyploid genomes and identical by descent shared tracts. Bioinformatics. 2013; 29(13):352\u201360. \n                    https:\/\/doi.org\/10.1093\/bioinformatics\/btt213\n                    \n                  .","journal-title":"Bioinformatics"},{"issue":"3","key":"2691_CR47","doi-asserted-by":"publisher","first-page":"e1003502","DOI":"10.1371\/journal.pcbi.1003502","volume":"10","author":"Emily Berger","year":"2014","unstructured":"Berger E, Yorukoglu D, Peng J, Berger B. Haptree: A novel Bayesian framework for single individual polyplotyping using NGS data. PLoS Comput Biol. 2014; 10(3):1003502. \n                    https:\/\/doi.org\/10.1371\/journal.pcbi.1003502\n                    \n                  .","journal-title":"PLoS Computational Biology"},{"issue":"4","key":"2691_CR48","doi-asserted-by":"publisher","first-page":"577","DOI":"10.1109\/TEVC.2013.2281535","volume":"18","author":"Kalyanmoy Deb","year":"2014","unstructured":"Deb K, Jain H. An evolutionary many-objective optimization algorithm using reference-point-based nondominated sorting approach, Part I: Solving problems with box constraints. IEEE Trans Evol Computat. 2014; 18(4):577\u2013601. \n                    https:\/\/doi.org\/10.1109\/TEVC.2013.2281535\n                    \n                  .","journal-title":"IEEE Transactions on Evolutionary Computation"},{"issue":"4","key":"2691_CR49","doi-asserted-by":"publisher","first-page":"635","DOI":"10.1038\/ng.3805","volume":"49","author":"Shicheng Guo","year":"2017","unstructured":"Guo S, Diep D, Plongthongkum N, Fung HL, Zhang K, Zhang K. Identification of methylation haplotype blocks aids in deconvolution of heterogeneous tissue samples and tumor tissue-of-origin mapping from plasma DNA. Nat Genet. 2017; 49(4):635\u201342. \n                    https:\/\/doi.org\/10.1038\/ng.3805\n                    \n                  .","journal-title":"Nature Genetics"},{"issue":"9","key":"2691_CR50","doi-asserted-by":"publisher","first-page":"e75146","DOI":"10.1371\/journal.pone.0075146","volume":"8","author":"Ivan Merelli","year":"2013","unstructured":"Merelli I, Li\u00f2 P, Milanesi L. NuChart: an R package to study gene spatial neighbourhoods with multi-omics annotations. PLoS ONE. 2013; 8(9):75146. \n                    https:\/\/doi.org\/10.1371\/journal.pone.0075146\n                    \n                  .","journal-title":"PLoS ONE"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-019-2691-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-019-2691-y\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-019-2691-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,4,16]],"date-time":"2020-04-16T23:05:54Z","timestamp":1587078354000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-019-2691-y"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,4]]},"references-count":50,"journal-issue":{"issue":"S4","published-print":{"date-parts":[[2019,4]]}},"alternative-id":["2691"],"URL":"https:\/\/doi.org\/10.1186\/s12859-019-2691-y","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,4]]},"assertion":[{"value":"18 April 2019","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare that they have no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}},{"value":"Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Publisher\u2019s Note"}}],"article-number":"172"}}