{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T00:28:12Z","timestamp":1773275292822,"version":"3.50.1"},"reference-count":38,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2011,1,5]],"date-time":"2011-01-05T00:00:00Z","timestamp":1294185600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2011,12]]},"DOI":"10.1186\/1471-2105-12-5","type":"journal-article","created":{"date-parts":[[2011,1,5]],"date-time":"2011-01-05T15:06:48Z","timestamp":1294240008000},"source":"Crossref","is-referenced-by-count":58,"title":["Combinatorial analysis and algorithms for quasispecies reconstruction using next-generation sequencing"],"prefix":"10.1186","volume":"12","author":[{"given":"Mattia CF","family":"Prosperi","sequence":"first","affiliation":[]},{"given":"Luciano","family":"Prosperi","sequence":"additional","affiliation":[]},{"given":"Alessandro","family":"Bruselles","sequence":"additional","affiliation":[]},{"given":"Isabella","family":"Abbate","sequence":"additional","affiliation":[]},{"given":"Gabriella","family":"Rozera","sequence":"additional","affiliation":[]},{"given":"Donatella","family":"Vincenti","sequence":"additional","affiliation":[]},{"given":"Maria Carmela","family":"Solmone","sequence":"additional","affiliation":[]},{"given":"Maria Rosaria","family":"Capobianchi","sequence":"additional","affiliation":[]},{"given":"Giovanni","family":"Ulivi","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2011,1,5]]},"reference":[{"key":"4322_CR1","unstructured":"Roche 454 GSFLX[\n                    http:\/\/www.454.com\/\n                    \n                  ]"},{"key":"4322_CR2","unstructured":"Illumina[\n                    http:\/\/www.illumina.com\/\n                    \n                  ]"},{"key":"4322_CR3","unstructured":"SOLiD[\n                    http:\/\/www3.appliedbiosystems.com\/AB_Home\/applicationstechnologies\/SOLiDSystemSequencing\/index.htm\n                    \n                  ]"},{"key":"4322_CR4","unstructured":"Helicos[\n                    http:\/\/www.helicosbio.com\/\n                    \n                  ]"},{"key":"4322_CR5","unstructured":"The Polonator[\n                    http:\/\/www.polonator.org\/\n                    \n                  ]"},{"key":"4322_CR6","doi-asserted-by":"publisher","first-page":"872","DOI":"10.1038\/nature06884","volume":"452","author":"DA Wheeler","year":"2008","unstructured":"Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A, He W, Chen YJ, Makhijani V, Rothberg JM: The complete genome of an individual by massively parallel DNA sequencing. Nature 2008, 452: 872\u2013876. 10.1038\/nature06884","journal-title":"Nature"},{"issue":"3","key":"4322_CR7","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1016\/j.tig.2007.12.007","volume":"24","author":"ER Mardis","year":"2008","unstructured":"Mardis ER: The impact of next-generation sequencing technology on genetics. Trends Genet 2008, 24(3):133\u201341.","journal-title":"Trends Genet"},{"issue":"4","key":"4322_CR8","doi-asserted-by":"publisher","first-page":"641","DOI":"10.1373\/clinchem.2008.112789","volume":"55","author":"KV Voelkerding","year":"2009","unstructured":"Voelkerding KV, Dames SA, Durtschi JD: Next-generation sequencing: from basic research to diagnostics. Clin Chem 2009, 55(4):641\u201358. 10.1373\/clinchem.2008.112789","journal-title":"Clin Chem"},{"issue":"1","key":"4322_CR9","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1038\/nrg2626","volume":"11","author":"ML Metzker","year":"2010","unstructured":"Metzker ML: Sequencing technologies - the next generation. Nat Rev Genet 2010, 11(1):31\u201346. 10.1038\/nrg2626","journal-title":"Nat Rev Genet"},{"issue":"24","key":"4322_CR10","doi-asserted-by":"publisher","first-page":"4992","DOI":"10.1093\/nar\/23.24.4992","volume":"23","author":"JK Bonfield","year":"1995","unstructured":"Bonfield JK, Smith K, Staden R: A new DNA sequence assembly program. Nucleic Acids Res 1995, 23(24):4992\u20139. 10.1093\/nar\/23.24.4992","journal-title":"Nucleic Acids Res"},{"key":"4322_CR11","doi-asserted-by":"publisher","first-page":"868","DOI":"10.1101\/gr.9.9.868","volume":"9","author":"X Huang","year":"1999","unstructured":"Huang X, Madan A: CAP3: A DNA sequence assembly program. Genome Research 1999, 9: 868\u2013877. 10.1101\/gr.9.9.868","journal-title":"Genome Research"},{"issue":"5461","key":"4322_CR12","doi-asserted-by":"publisher","first-page":"2196","DOI":"10.1126\/science.287.5461.2196","volume":"287","author":"EW Myers","year":"2000","unstructured":"Myers EW, Sutton GG, Delcher AL, Dew IM, Fasulo DP, Flanigan MJ, Kravitz SA, Mobarry CM, Reinert KH, Venter JC, et al.: A whole-genome assembly of Drosophila. Science 2000, 287(5461):2196\u2013204. 10.1126\/science.287.5461.2196","journal-title":"Science"},{"key":"4322_CR13","doi-asserted-by":"publisher","first-page":"177","DOI":"10.1101\/gr.208902","volume":"12","author":"S Batzoglou","year":"2002","unstructured":"Batzoglou S, Jaffe DB, Stanley K, Butler J, Gnerre S, Mauceli E, Berger B, Mesirov JP, Lander ES: ARACHNE: a whole-genome shotgun assembler. Genome Research 2002, 12: 177\u2013189. 10.1101\/gr.208902","journal-title":"Genome Research"},{"issue":"1","key":"4322_CR14","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1016\/S0169-2607(01)00194-8","volume":"70","author":"MT Tammi","year":"2003","unstructured":"Tammi MT, Arner E, Andersson B: TRAP: Tandem Repeat Assembly Program produces improved shotgun assemblies of repetitive sequences. Computational Methods Programs Biomed 2003, 70(1):47\u201359. 10.1016\/S0169-2607(01)00194-8","journal-title":"Computational Methods Programs Biomed"},{"issue":"11","key":"4322_CR15","doi-asserted-by":"publisher","first-page":"1697","DOI":"10.1101\/gr.6435207","volume":"17","author":"JC Dohm","year":"2007","unstructured":"Dohm JC, Lottaz C, Borodina T, Himmelbauer H: SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. Genome Research 2007, 17(11):1697\u2013706. 10.1101\/gr.6435207","journal-title":"Genome Research"},{"key":"4322_CR16","doi-asserted-by":"publisher","first-page":"1851","DOI":"10.1101\/gr.078212.108","volume":"18","author":"H Li","year":"2008","unstructured":"Li H, Ruan J, Durbin R: Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Research 2008, 18: 1851\u20131858. 10.1101\/gr.078212.108","journal-title":"Genome Research"},{"key":"4322_CR17","doi-asserted-by":"publisher","first-page":"1638","DOI":"10.1101\/gr.077776.108","volume":"18","author":"DR Smith","year":"2008","unstructured":"Smith DR, Quinlan AR, Peckham HE, Makowsky K, Tao W, Woolf B, Shen L, Donahue WF, Tusneem N, Richardson PM, et al.: Rapid whole-genome mutational profiling using next-generation sequencing technologies. Genome Research 2008, 18: 1638\u20131642. 10.1101\/gr.077776.108","journal-title":"Genome Research"},{"issue":"24","key":"4322_CR18","doi-asserted-by":"publisher","first-page":"2818","DOI":"10.1093\/bioinformatics\/btn548","volume":"24","author":"JR Miller","year":"2008","unstructured":"Miller JR, Delcher AL, Koren S, Venter E, Walenz BP, Brownley A, Johnson J, Li K, Mobarry C, Sutton G: Aggressive assembly of pyrosequencing reads with mates. Bioinformatics 2008, 24(24):2818\u201324. 10.1093\/bioinformatics\/btn548","journal-title":"Bioinformatics"},{"issue":"7","key":"4322_CR19","doi-asserted-by":"publisher","first-page":"R143","DOI":"10.1186\/gb-2007-8-7-r143","volume":"8","author":"SM Huse","year":"2007","unstructured":"Huse SM, Huber JA, Morrison HG, Sogin ML, Welch DM: Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol 2007, 8(7):R143. 10.1186\/gb-2007-8-7-r143","journal-title":"Genome Biol"},{"issue":"15","key":"4322_CR20","doi-asserted-by":"publisher","first-page":"e104","DOI":"10.1093\/nar\/gkp492","volume":"37","author":"N Philippe","year":"2009","unstructured":"Philippe N, Boureux A, Br\u00e9h\u00e9lin L, Tarhio J, Commes T, Rivals E: Using reads to annotate the genome: influence of length, background distribution, and sequence errors on prediction capacity. Nucleic Acids Res 2009, 37(15):e104. 10.1093\/nar\/gkp492","journal-title":"Nucleic Acids Res"},{"issue":"8","key":"4322_CR21","doi-asserted-by":"publisher","first-page":"1195","DOI":"10.1101\/gr.6468307","volume":"17","author":"C Wang","year":"2007","unstructured":"Wang C, Mitsuya Y, Gharizadeh B, Ronaghi M, Shafer RW: Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance. Genome Research 2007, 17(8):1195\u2013201. 10.1101\/gr.6468307","journal-title":"Genome Research"},{"issue":"4","key":"4322_CR22","doi-asserted-by":"publisher","first-page":"1718","DOI":"10.1128\/JVI.02011-08","volume":"83","author":"M Solmone","year":"2009","unstructured":"Solmone M, Vincenti D, Prosperi MC, Bruselles A, Ippolito G, Capobianchi MR: Use of massively parallel ultradeep pyrosequencing to characterize the genetic diversity of hepatitis B virus in drug-resistant and drug-naive patients and to detect minor variants in reverse transcriptase and hepatitis B s antigen. J Virol 2009, 83(4):1718\u201326. 10.1128\/JVI.02011-08","journal-title":"J Virol"},{"key":"4322_CR23","first-page":"114","volume":"13","author":"V Jojic","year":"2008","unstructured":"Jojic V, Hertz T, Jojic N: Population sequencing using short reads: HIV as a case study. Pacific Symposium on Biocomputing 2008, 13: 114\u2013125.","journal-title":"Pacific Symposium on Biocomputing"},{"issue":"4","key":"4322_CR24","doi-asserted-by":"publisher","first-page":"e1000074","DOI":"10.1371\/journal.pcbi.1000074","volume":"4","author":"N Eriksson","year":"2008","unstructured":"Eriksson N, Pachter L, Mitsuya Y, Rhee SY, Wang C, Gharizadeh B, Ronaghi M, Shafer RW, Beerenwinkel N: Viral population estimation using pyrosequencing. PLoS Comput Biol 2008, 4(4):e1000074. 10.1371\/journal.pcbi.1000074","journal-title":"PLoS Comput Biol"},{"key":"4322_CR25","doi-asserted-by":"publisher","first-page":"159","DOI":"10.1007\/978-3-540-79450-9_15","volume-title":"Proc. of International Symposium on Bioinformatics Research & Applications, LNBI","author":"K Wesbrooks","year":"2008","unstructured":"Wesbrooks K, Astrovskaya I, Rendon DC, Khudyakov Y, Berman P, Zelikovsky A: HCV Quasispecies Assembly using Network Flows. In Proc. of International Symposium on Bioinformatics Research & Applications, LNBI. Volume 4983. Springer Berlin\/Heidelberg; 2008:159\u2013170."},{"key":"4322_CR26","unstructured":"ShoRAH[\n                    http:\/\/www.bsse.ethz.ch\/cbg\/software\/shorah\n                    \n                  ]"},{"key":"4322_CR27","first-page":"345","volume-title":"LNCS","author":"O Zagordi","year":"2009","unstructured":"Zagordi O, Geyrhofer L, Roth V, Beerenwinkel N: Deep sequencing of a genetically heterogeneous sample: local variant reconstruction and read error correction. In LNCS. Volume 5541. Springer Berlin\/Heidelberg; 2009:345\u2013358."},{"issue":"35","key":"4322_CR28","doi-asserted-by":"publisher","first-page":"13081","DOI":"10.1073\/pnas.0801523105","volume":"105","author":"PJ Campbell","year":"2008","unstructured":"Campbell PJ, Pleasance ED, Stephens PJ, Dicks E, Rance R, Goodhead I, Follows GA, Green AR, Futreal PA, Stratton MR: Subclonal phylogenetic structures in cancer revealed by ultra-deep sequencing. Proc Natl Acad Sci USA 2008, 105(35):13081\u20136. 10.1073\/pnas.0801523105","journal-title":"Proc Natl Acad Sci USA"},{"issue":"3","key":"4322_CR29","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1038\/nmeth.1184","volume":"5","author":"M Hamady","year":"2008","unstructured":"Hamady M, Walker JJ, Harris JK, Gold NJ, Knight R: Error correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nature Methods 2008, 5(3):235\u2013237. 10.1038\/nmeth.1184","journal-title":"Nature Methods"},{"issue":"19","key":"4322_CR30","doi-asserted-by":"publisher","first-page":"e130","DOI":"10.1093\/nar\/gkm760","volume":"35","author":"P Parameswaran","year":"2007","unstructured":"Parameswaran P, Jalili R, Tao L, Shokralla S, Gharizadeh B, Ronaghi M, Fire AZ: A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing. Nucleic Acids Res 2007, 35(19):e130. 10.1093\/nar\/gkm760","journal-title":"Nucleic Acids Res"},{"key":"4322_CR31","doi-asserted-by":"publisher","first-page":"401","DOI":"10.1016\/S0097-8485(01)00074-2","volume":"25","author":"JN Bacro","year":"2000","unstructured":"Bacro JN, Comet JP: Sequence alignment: an approximation law for the Z-value with applications to databank scanning. Computers and Chemistry 2000, 25: 401\u2013410. 10.1016\/S0097-8485(01)00074-2","journal-title":"Computers and Chemistry"},{"key":"4322_CR32","doi-asserted-by":"publisher","first-page":"705","DOI":"10.1016\/0022-2836(82)90398-9","volume":"162","author":"O Gotoh","year":"1982","unstructured":"Gotoh O: An improved algorithm for matching biological sequences. J Mol Biol 1982, 162: 705\u2013708. 10.1016\/0022-2836(82)90398-9","journal-title":"J Mol Biol"},{"key":"4322_CR33","first-page":"149","volume":"75","author":"M Eigen","year":"1989","unstructured":"Eigen M, McCaskill J, Schuster P: The molecular quasi-species. Adv Chem Phys 1989, 75: 149\u2013263. full_text","journal-title":"Adv Chem Phys"},{"key":"4322_CR34","doi-asserted-by":"publisher","first-page":"151","DOI":"10.1146\/annurev.micro.51.1.151","volume":"51","author":"E Domingo","year":"1997","unstructured":"Domingo E, Holland JJ: RNA virus mutations and fitness for survival. Annu Rev Microbiol 1997, 51: 151\u2013178. 10.1146\/annurev.micro.51.1.151","journal-title":"Annu Rev Microbiol"},{"key":"4322_CR35","doi-asserted-by":"publisher","first-page":"231","DOI":"10.1016\/0888-7543(88)90007-9","volume":"2","author":"ES Lander","year":"1988","unstructured":"Lander ES, Waterman MS: Genomic mapping by fingerprinting random clones: a mathematical analysis. Genomics 1988, 2: 231\u2013239. 10.1016\/0888-7543(88)90007-9","journal-title":"Genomics"},{"key":"4322_CR36","doi-asserted-by":"publisher","first-page":"e24","DOI":"10.1371\/journal.pcbi.0010024","volume":"1","author":"K Chen","year":"2005","unstructured":"Chen K, Pachter L: Bioinformatics for whole-genome shotgun sequencing of microbial communities. PLoS Comput Biol 2005, 1: e24. 10.1371\/journal.pcbi.0010024","journal-title":"PLoS Comput Biol"},{"issue":"3","key":"4322_CR37","doi-asserted-by":"publisher","first-page":"457","DOI":"10.1214\/aos\/1176345003","volume":"8","author":"J Berkson","year":"1980","unstructured":"Berkson J: Minimum Chi-Square, not Maximum Likelihood! Ann Statist 1980, 8(3):457\u2013487. 10.1214\/aos\/1176345003","journal-title":"Ann Statist"},{"issue":"1","key":"4322_CR38","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1007\/BF01188580","volume":"13","author":"JD Kececioglu","year":"1999","unstructured":"Kececioglu JD, Myers EW: Combinatorial algorithms for DNA sequence assembly. Algorithmica 1999, 13(1):7\u201351. 10.1007\/BF01188580","journal-title":"Algorithmica"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-12-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-12-5\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-12-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,22]],"date-time":"2019-01-22T09:14:24Z","timestamp":1548148464000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-12-5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,1,5]]},"references-count":38,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2011,12]]}},"alternative-id":["4322"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-12-5","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,1,5]]},"article-number":"5"}}