{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,4]],"date-time":"2025-11-04T15:53:24Z","timestamp":1762271604748},"reference-count":39,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2012,3,23]],"date-time":"2012-03-23T00:00:00Z","timestamp":1332460800000},"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":[[2012,12]]},"DOI":"10.1186\/1471-2105-13-47","type":"journal-article","created":{"date-parts":[[2012,3,23]],"date-time":"2012-03-23T14:35:57Z","timestamp":1332513357000},"source":"Crossref","is-referenced-by-count":53,"title":["Analysis of high-depth sequence data for studying viral diversity: a comparison of next generation sequencing platforms using Segminator II"],"prefix":"10.1186","volume":"13","author":[{"given":"John","family":"Archer","sequence":"first","affiliation":[]},{"given":"Greg","family":"Baillie","sequence":"additional","affiliation":[]},{"given":"Simon J","family":"Watson","sequence":"additional","affiliation":[]},{"given":"Paul","family":"Kellam","sequence":"additional","affiliation":[]},{"given":"Andrew","family":"Rambaut","sequence":"additional","affiliation":[]},{"given":"David L","family":"Robertson","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2012,3,23]]},"reference":[{"key":"5184_CR1","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1016\/j.jbiotec.2008.03.021","volume":"136","author":"M Droege","year":"2008","unstructured":"Droege M, Hill B: The Genome Sequencer FLX System-longer reads, more applications, straight forward bioinformatics and more complete data sets. J Biotechnol 2008, 136: 3\u201310. 10.1016\/j.jbiotec.2008.03.021","journal-title":"J Biotechnol"},{"key":"5184_CR2","doi-asserted-by":"publisher","first-page":"433","DOI":"10.1517\/14622416.5.4.433","volume":"5","author":"S Bennett","year":"2004","unstructured":"Bennett S: Solexa Ltd. Pharmacogenomics 2004, 5: 433\u2013438. 10.1517\/14622416.5.4.433","journal-title":"Pharmacogenomics"},{"key":"5184_CR3","doi-asserted-by":"publisher","first-page":"e1001022","DOI":"10.1371\/journal.pcbi.1001022","volume":"6","author":"J Archer","year":"2010","unstructured":"Archer J, Rambaut A, Taillon BE, Harrigan PR, Lewis M, Robertson DL: The evolutionary analysis of emerging low frequency HIV-1 CXCR4 using variants through time-an ultra-deep approach. PLoS Comput Biol 2010, 6: e1001022. 10.1371\/journal.pcbi.1001022","journal-title":"PLoS Comput Biol"},{"key":"5184_CR4","doi-asserted-by":"publisher","first-page":"987","DOI":"10.1038\/ng.195","volume":"40","author":"KE Holt","year":"2008","unstructured":"Holt KE, Parkhill J, Mazzoni CJ, Roumagnac P, Weill FX, Goodhead I, Rance R, Baker S, Maskell DJ, Wain J, et al.: High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. Nat Genet 2008, 40: 987\u2013993. 10.1038\/ng.195","journal-title":"Nat Genet"},{"key":"5184_CR5","doi-asserted-by":"publisher","first-page":"e10256","DOI":"10.1371\/journal.pone.0010256","volume":"5","author":"M Kuroda","year":"2010","unstructured":"Kuroda M, Katano H, Nakajima N, Tobiume M, Ainai A, Sekizuka T, Hasegawa H, Tashiro M, Sasaki Y, Arakawa Y, et al.: Characterization of quasispecies of pandemic 2009 influenza A virus (A\/H1N1\/2009) by de novo sequencing using a next-generation DNA sequencer. PLoS One 2010, 5: e10256. 10.1371\/journal.pone.0010256","journal-title":"PLoS One"},{"key":"5184_CR6","doi-asserted-by":"publisher","first-page":"819","DOI":"10.1093\/molbev\/msp289","volume":"27","author":"AF Poon","year":"2009","unstructured":"Poon AF, Swenson LC, Dong WW, Deng W, Kosakovsky Pond SL, Brumme ZL, Mullins JI, Richman DD, Harrigan PR, Frost SD: Phylogenetic analysis of population-based and deep sequencing data to identify coevolving sites in the nef gene of HIV-1. Mol Biol Evol 2009, 27: 819\u2013832.","journal-title":"Mol Biol Evol"},{"key":"5184_CR7","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 Res 2007, 17: 1195\u20131201. 10.1101\/gr.6468307","journal-title":"Genome Res"},{"key":"5184_CR8","doi-asserted-by":"publisher","first-page":"484","DOI":"10.2353\/jmoldx.2008.080027","volume":"10","author":"JR ten Bosch","year":"2008","unstructured":"ten Bosch JR, Grody WW: Keeping up with the next generation: massively parallel sequencing in clinical diagnostics. J Mol Diagn 2008, 10: 484\u2013492. 10.2353\/jmoldx.2008.080027","journal-title":"J Mol Diagn"},{"key":"5184_CR9","doi-asserted-by":"publisher","first-page":"e197","DOI":"10.1371\/journal.pone.0000197","volume":"2","author":"J Binladen","year":"2007","unstructured":"Binladen J, Gilbert MT, Bollback JP, Panitz F, Bendixen C, Nielsen R, Willerslev E: The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS One 2007, 2: e197. 10.1371\/journal.pone.0000197","journal-title":"PLoS One"},{"key":"5184_CR10","doi-asserted-by":"publisher","first-page":"267","DOI":"10.1038\/nprot.2007.520","volume":"3","author":"M Meyer","year":"2008","unstructured":"Meyer M, Stenzel U, Hofreiter M: Parallel tagged sequencing on the 454 platform. Nat Protoc 2008, 3: 267\u2013278. 10.1038\/nprot.2007.520","journal-title":"Nat Protoc"},{"key":"5184_CR11","first-page":"287","volume":"121","author":"RB Lal","year":"2005","unstructured":"Lal RB, Chakrabarti S, Yang C: Impact of genetic diversity of HIV-1 on diagnosis, antiretroviral therapy & vaccine development. Indian J Med Res 2005, 121: 287\u2013314.","journal-title":"Indian J Med Res"},{"key":"5184_CR12","doi-asserted-by":"publisher","first-page":"e1000565","DOI":"10.1371\/journal.pcbi.1000565","volume":"5","author":"F Luciani","year":"2009","unstructured":"Luciani F, Alizon S: The evolutionary dynamics of a rapidly mutating virus within and between hosts: the case of hepatitis C virus. PLoS Comput Biol 2009, 5: e1000565. 10.1371\/journal.pcbi.1000565","journal-title":"PLoS Comput Biol"},{"key":"5184_CR13","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1186\/1471-2148-11-62","volume":"11","author":"L Tazi","year":"2011","unstructured":"Tazi L, Imamichi H, Hirschfeld S, Metcalf JA, Orsega S, Perez-Losada M, Posada D, Lane HC, Crandall KA: HIV-1 infected monozygotic twins: a tale of two outcomes. BMC Evol Biol 2011, 11: 62. 10.1186\/1471-2148-11-62","journal-title":"BMC Evol Biol"},{"key":"5184_CR14","doi-asserted-by":"publisher","first-page":"4909","DOI":"10.1128\/JVI.80.10.4909-4920.2006","volume":"80","author":"M Westby","year":"2006","unstructured":"Westby M, Lewis M, Whitcomb J, Youle M, Pozniak AL, James IT, Jenkins TM, Perros M, van der Ryst E: Emergence of CXCR4-using human immunodeficiency virus type 1 (HIV-1) variants in a minority of HIV-1-infected patients following treatment with the CCR5 antagonist maraviroc is from a pretreatment CXCR4-using virus reservoir. J Virol 2006, 80: 4909\u20134920. 10.1128\/JVI.80.10.4909-4920.2006","journal-title":"J Virol"},{"key":"5184_CR15","doi-asserted-by":"publisher","first-page":"1411","DOI":"10.1097\/QAD.0b013e3282fc972e","volume":"22","author":"FD Bushman","year":"2008","unstructured":"Bushman FD, Hoffmann C, Ronen K, Malani N, Minkah N, Rose HM, Tebas P, Wang GP: Massively parallel pyrosequencing in HIV research. AIDS 2008, 22: 1411\u20131415. 10.1097\/QAD.0b013e3282fc972e","journal-title":"AIDS"},{"key":"5184_CR16","doi-asserted-by":"publisher","first-page":"1135","DOI":"10.1038\/nbt1486","volume":"26","author":"J Shendure","year":"2008","unstructured":"Shendure J, Hanlee J: Next-generation DNA sequencing. Nat Biotech 2008, 26: 1135\u20131145. 10.1038\/nbt1486","journal-title":"Nat Biotech"},{"key":"5184_CR17","doi-asserted-by":"publisher","first-page":"e5683","DOI":"10.1371\/journal.pone.0005683","volume":"4","author":"AM Tsibris","year":"2009","unstructured":"Tsibris AM, Korber B, Arnaout R, Russ C, Lo CC, Leitner T, Gaschen B, Theiler J, Paredes R, Su Z, et al.: Quantitative deep sequencing reveals dynamic HIV-1 escape and large population shifts during CCR5 antagonist therapy in vivo. PLoS One 2009, 4: e5683. 10.1371\/journal.pone.0005683","journal-title":"PLoS One"},{"key":"5184_CR18","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1186\/1742-4690-6-15","volume":"6","author":"G Rozera","year":"2009","unstructured":"Rozera G, Abbate I, Bruselles A, Vlassi C, D'Offizi G, Narciso P, Chillemi G, Prosperi M, Ippolito G, Capobianchi MR: Massively parallel pyrosequencing highlights minority variants in the HIV-1 env quasispecies deriving from lymphomonocyte sub-populations. Retrovirology 2009, 6: 15. 10.1186\/1742-4690-6-15","journal-title":"Retrovirology"},{"key":"5184_CR19","doi-asserted-by":"publisher","first-page":"487","DOI":"10.1038\/ng.795","volume":"43","author":"T Hinkley","year":"2011","unstructured":"Hinkley T, Martins J, Chappey C, Haddad M, Stawiski E, Whitcomb JM, Petropoulos CJ, Bonhoeffer S: A systems analysis of mutational effects in HIV-1 protease and reverse transcriptase. Nat Genet 2011, 43: 487\u2013489. 10.1038\/ng.795","journal-title":"Nat Genet"},{"key":"5184_CR20","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1093\/bmb\/58.1.19","volume":"58","author":"B Korber","year":"2001","unstructured":"Korber B, Gaschen B, Yusim K, Thakallapally R, Kesmir C, Detours V: Evolutionary and immunological implications of contemporary HIV-1 variation. Br Med Bull 2001, 58: 19\u201342. 10.1093\/bmb\/58.1.19","journal-title":"Br Med Bull"},{"key":"5184_CR21","first-page":"67","volume":"10","author":"RW Shafer","year":"2008","unstructured":"Shafer RW, Schapiro JM: HIV-1 drug resistance mutations: an updated framework for the second decade of HAART. AIDS Rev 2008, 10: 67\u201384.","journal-title":"AIDS Rev"},{"key":"5184_CR22","doi-asserted-by":"publisher","first-page":"319","DOI":"10.1038\/nm.2089","volume":"16","author":"DH Barouch","year":"2010","unstructured":"Barouch DH, O'Brien KL, Simmons NL, King SL, Abbink P, Maxfield LF, Sun YH, La Porte A, Riggs AM, Lynch DM, et al.: Mosaic HIV-1 vaccines expand the breadth and depth of cellular immune responses in rhesus monkeys. Nat Med 2010, 16: 319\u2013323. 10.1038\/nm.2089","journal-title":"Nat Med"},{"key":"5184_CR23","doi-asserted-by":"publisher","first-page":"100","DOI":"10.1038\/nm1461","volume":"13","author":"W Fischer","year":"2007","unstructured":"Fischer W, Perkins S, Theiler J, Bhattacharya T, Yusim K, Funkhouser R, Kuiken C, Haynes B, Letvin NL, Walker BD, et al.: Polyvalent vaccines for optimal coverage of potential T-cell epitopes in global HIV-1 variants. Nat Med 2007, 13: 100\u2013106. 10.1038\/nm1461","journal-title":"Nat Med"},{"key":"5184_CR24","doi-asserted-by":"publisher","first-page":"142","DOI":"10.1016\/j.tig.2007.12.006","volume":"24","author":"M Pop","year":"2008","unstructured":"Pop M, Salzberg SL: Bioinformatics challenges of new sequencing technology. Trends Genet 2008, 24: 142\u2013149. 10.1016\/j.tig.2007.12.006","journal-title":"Trends Genet"},{"key":"5184_CR25","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1186\/1471-2164-12-245","volume":"12","author":"A Gilles","year":"2011","unstructured":"Gilles A, Meglecz E, Pech N, Ferreira S, Malausa T, Martin JF: Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing. BMC Genomics 2011, 12: 245. 10.1186\/1471-2164-12-245","journal-title":"BMC Genomics"},{"key":"5184_CR26","doi-asserted-by":"publisher","first-page":"e90","DOI":"10.1093\/nar\/gkr344","volume":"39","author":"K Nakamura","year":"2011","unstructured":"Nakamura K, Oshima T, Morimoto T, Ikeda S, Yoshikawa H, Shiwa Y, Ishikawa S, Linak MC, Hirai A, Takahashi H, et al.: Sequence-specific error profile of Illumina sequencers. Nucleic Acids Res 2011, 39: e90. 10.1093\/nar\/gkr344","journal-title":"Nucleic Acids Res"},{"key":"5184_CR27","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 PC, Strausberg RL, Wang X, Stockwell TB, Beeson KY, Schork NJ, Murray SS, Topol EJ, Levy S, et al.: 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":"5184_CR28","doi-asserted-by":"publisher","first-page":"387","DOI":"10.1146\/annurev.genom.9.081307.164359","volume":"9","author":"ER Mardis","year":"2008","unstructured":"Mardis ER: Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 2008, 9: 387\u2013402. 10.1146\/annurev.genom.9.081307.164359","journal-title":"Annu Rev Genomics Hum Genet"},{"key":"5184_CR29","doi-asserted-by":"publisher","first-page":"763","DOI":"10.1101\/gr.070227.107","volume":"18","author":"W Brockman","year":"2008","unstructured":"Brockman W, Alvarez P, Young S, Garber M, Giannoukos G, Lee WL, Russ C, Lander ES, Nusbaum C, Jaffe DB: Quality scores and SNP detection in sequencing-by-synthesis systems. Genome Res 2008, 18: 763\u2013770. 10.1101\/gr.070227.107","journal-title":"Genome Res"},{"key":"5184_CR30","doi-asserted-by":"publisher","first-page":"406","DOI":"10.1038\/jhg.2011.43","volume":"56","author":"S Bao","year":"2011","unstructured":"Bao S, Jiang R, Kwan W, Wang B, Ma X, Song YQ: Evaluation of next-generation sequencing software in mapping and assembly. J Hum Genet 2011, 56: 406\u2013414. 10.1038\/jhg.2011.43","journal-title":"J Hum Genet"},{"key":"5184_CR31","doi-asserted-by":"publisher","first-page":"220","DOI":"10.1186\/gb-2010-11-12-220","volume":"11","author":"A Oshlack","year":"2010","unstructured":"Oshlack A, Robinson MD, Young MD: From RNA-seq reads to differential expression results. Genome Biol 2010, 11: 220. 10.1186\/gb-2010-11-12-220","journal-title":"Genome Biol"},{"key":"5184_CR32","unstructured":"Geneious v5.4[\n                    http:\/\/www.geneious.com\/\n                    \n                  ]"},{"key":"5184_CR33","doi-asserted-by":"publisher","first-page":"10309","DOI":"10.1128\/JVI.01109-09","volume":"83","author":"B Zhou","year":"2009","unstructured":"Zhou B, Donnelly ME, Scholes DT, St George K, Hatta M, Kawaoka Y, Wentworth DE: Single-reaction genomic amplification accelerates sequencing and vaccine production for classical and Swine origin human influenza a viruses. J Virol 2009, 83: 10309\u201310313. 10.1128\/JVI.01109-09","journal-title":"J Virol"},{"key":"5184_CR34","doi-asserted-by":"publisher","first-page":"1792","DOI":"10.1093\/nar\/gkh340","volume":"32","author":"RC Edgar","year":"2004","unstructured":"Edgar RC: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004, 32: 1792\u20131797. 10.1093\/nar\/gkh340","journal-title":"Nucleic Acids Res"},{"key":"5184_CR35","doi-asserted-by":"publisher","first-page":"1209","DOI":"10.1097\/QAD.0b013e32832b4399","volume":"23","author":"J Archer","year":"2009","unstructured":"Archer J, Braverman MS, Taillon BE, Desany B, James I, Harrigan PR, Lewis M, Robertson DL: Detection of low-frequency pretherapy chemokine (CXC motif) receptor 4 (CXCR4)-using HIV-1 with ultra-deep pyrosequencing. AIDS 2009, 23: 1209\u20131218. 10.1097\/QAD.0b013e32832b4399","journal-title":"AIDS"},{"key":"5184_CR36","doi-asserted-by":"publisher","first-page":"1157","DOI":"10.1093\/bioinformatics\/btr076","volume":"27","author":"H Li","year":"2011","unstructured":"Li H: Improving SNP discovery by base alignment quality. Bioinformatics 2011, 27: 1157\u20131158. 10.1093\/bioinformatics\/btr076","journal-title":"Bioinformatics"},{"key":"5184_CR37","doi-asserted-by":"publisher","first-page":"179","DOI":"10.1038\/nmeth.1172","volume":"5","author":"AR Quinlan","year":"2008","unstructured":"Quinlan AR, Stewart DA, Stromberg MP, Marth GT: Pyrobayes: an improved base caller for SNP discovery in pyrosequences. Nat Methods 2008, 5: 179\u2013181. 10.1038\/nmeth.1172","journal-title":"Nat Methods"},{"key":"5184_CR38","doi-asserted-by":"publisher","first-page":"1455","DOI":"10.1093\/bioinformatics\/btr170","volume":"27","author":"L Salmela","year":"2011","unstructured":"Salmela L, Schroder J: Correcting errors in short reads by multiple alignments. Bioinformatics 2011, 27: 1455\u201361. 10.1093\/bioinformatics\/btr170","journal-title":"Bioinformatics"},{"key":"5184_CR39","doi-asserted-by":"publisher","first-page":"7400","DOI":"10.1093\/nar\/gkq655","volume":"38","author":"O Zagordi","year":"2010","unstructured":"Zagordi O, Klein R, Daumer M, Beerenwinkel N: Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies. Nucleic Acids Res 2010, 38: 7400\u20137409. 10.1093\/nar\/gkq655","journal-title":"Nucleic Acids Res"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-13-47.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-13-47\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-13-47.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,23]],"date-time":"2019-01-23T05:53:25Z","timestamp":1548222805000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-13-47"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,3,23]]},"references-count":39,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2012,12]]}},"alternative-id":["5184"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-13-47","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,3,23]]},"article-number":"47"}}