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PCR-induced transitions are the major source of error in cleaned ultra-deep pyrosequencing data.

Brodin J, Mild M, Hedskog C, Sherwood E, Leitner T, Andersson B, Albert J.

PLoS One. 2013 Jul 23;8(7):e70388. doi: 10.1371/journal.pone.0070388. Print 2013.


Performance of ultra-deep pyrosequencing in analysis of HIV-1 pol gene variation.

Mild M, Hedskog C, Jernberg J, Albert J.

PLoS One. 2011;6(7):e22741. doi: 10.1371/journal.pone.0022741. Epub 2011 Jul 25.


Analysis of 454 sequencing error rate, error sources, and artifact recombination for detection of Low-frequency drug resistance mutations in HIV-1 DNA.

Shao W, Boltz VF, Spindler JE, Kearney MF, Maldarelli F, Mellors JW, Stewart C, Volfovsky N, Levitsky A, Stephens RM, Coffin JM.

Retrovirology. 2013 Feb 13;10:18. doi: 10.1186/1742-4690-10-18.


Ultra-deep pyrosequencing (UDPS) data treatment to study amplicon HCV minor variants.

Gregori J, Esteban JI, Cubero M, Garcia-Cehic D, Perales C, Casillas R, Alvarez-Tejado M, Rodríguez-Frías F, Guardia J, Domingo E, Quer J.

PLoS One. 2013 Dec 31;8(12):e83361. doi: 10.1371/journal.pone.0083361. eCollection 2013.


Dynamics of HIV-1 quasispecies during antiviral treatment dissected using ultra-deep pyrosequencing.

Hedskog C, Mild M, Jernberg J, Sherwood E, Bratt G, Leitner T, Lundeberg J, Andersson B, Albert J.

PLoS One. 2010 Jul 7;5(7):e11345. doi: 10.1371/journal.pone.0011345.


'Sentinel' mutations in standard population sequencing can predict the presence of HIV-1 reverse transcriptase major mutations detectable only by ultra-deep pyrosequencing.

Alteri C, Santoro MM, Abbate I, Rozera G, Bruselles A, Bartolini B, Gori C, Forbici F, Orchi N, Tozzi V, Palamara G, Antinori A, Narciso P, Girardi E, Svicher V, Ceccherini-Silberstein F, Capobianchi MR, Perno CF.

J Antimicrob Chemother. 2011 Nov;66(11):2615-23. doi: 10.1093/jac/dkr354. Epub 2011 Sep 2.


Quality score based identification and correction of pyrosequencing errors.

Iyer S, Bouzek H, Deng W, Larsen B, Casey E, Mullins JI.

PLoS One. 2013 Sep 5;8(9):e73015. doi: 10.1371/journal.pone.0073015. eCollection 2013.


Challenges with using primer IDs to improve accuracy of next generation sequencing.

Brodin J, Hedskog C, Heddini A, Benard E, Neher RA, Mild M, Albert J.

PLoS One. 2015 Mar 5;10(3):e0119123. doi: 10.1371/journal.pone.0119123. eCollection 2015.


Improved detection of rare HIV-1 variants using 454 pyrosequencing.

Larsen BB, Chen L, Maust BS, Kim M, Zhao H, Deng W, Westfall D, Beck I, Frenkel LM, Mullins JI.

PLoS One. 2013 Oct 2;8(10):e76502. doi: 10.1371/journal.pone.0076502. eCollection 2013.


Identification and correction of systematic error in high-throughput sequence data.

Meacham F, Boffelli D, Dhahbi J, Martin DI, Singer M, Pachter L.

BMC Bioinformatics. 2011 Nov 21;12:451. doi: 10.1186/1471-2105-12-451.


Next-generation sequencing of HIV-1 RNA genomes: determination of error rates and minimizing artificial recombination.

Di Giallonardo F, Zagordi O, Duport Y, Leemann C, Joos B, Künzli-Gontarczyk M, Bruggmann R, Beerenwinkel N, Günthard HF, Metzner KJ.

PLoS One. 2013 Sep 18;8(9):e74249. doi: 10.1371/journal.pone.0074249. eCollection 2013.


Nucleic acid template and the risk of a PCR-Induced HIV-1 drug resistance mutation.

Varghese V, Wang E, Babrzadeh F, Bachmann MH, Shahriar R, Liu T, Mappala SJ, Gharizadeh B, Fessel WJ, Katzenstein D, Kassaye S, Shafer RW.

PLoS One. 2010 Jun 7;5(6):e10992. doi: 10.1371/journal.pone.0010992.


Analysis of ultra-deep pyrosequencing and cloning based sequencing of the basic core promoter/precore/core region of hepatitis B virus using newly developed bioinformatics tools.

Yousif M, Bell TG, Mudawi H, Glebe D, Kramvis A.

PLoS One. 2014 Apr 16;9(4):e95377. doi: 10.1371/journal.pone.0095377. eCollection 2014.


Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies.

Zagordi O, Klein R, Däumer M, Beerenwinkel N.

Nucleic Acids Res. 2010 Nov;38(21):7400-9. doi: 10.1093/nar/gkq655. Epub 2010 Jul 29.


Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and genome analyzer systems.

Minoche AE, Dohm JC, Himmelbauer H.

Genome Biol. 2011 Nov 8;12(11):R112. doi: 10.1186/gb-2011-12-11-r112.


A comparative study of ultra-deep pyrosequencing and cloning to quantitatively analyze the viral quasispecies using hepatitis B virus infection as a model.

Ramírez C, Gregori J, Buti M, Tabernero D, Camós S, Casillas R, Quer J, Esteban R, Homs M, Rodriguez-Frías F.

Antiviral Res. 2013 May;98(2):273-83. doi: 10.1016/j.antiviral.2013.03.007. Epub 2013 Mar 20.


Indel and Carryforward Correction (ICC): a new analysis approach for processing 454 pyrosequencing data.

Deng W, Maust BS, Westfall DH, Chen L, Zhao H, Larsen BB, Iyer S, Liu Y, Mullins JI.

Bioinformatics. 2013 Oct 1;29(19):2402-9. doi: 10.1093/bioinformatics/btt434. Epub 2013 Jul 29.


Minor variant detection in amplicons using 454 massive parallel pyrosequencing: experiences and considerations for successful applications.

Vandenbroucke I, Van Marck H, Verhasselt P, Thys K, Mostmans W, Dumont S, Van Eygen V, Coen K, Tuefferd M, Aerssens J.

Biotechniques. 2011 Sep;51(3):167-77. doi: 10.2144/000113733.


Minority variants associated with resistance to HIV-1 nonnucleoside reverse transcriptase inhibitors during primary infection.

Nicot F, Saliou A, Raymond S, Sauné K, Dubois M, Massip P, Marchou B, Delobel P, Izopet J.

J Clin Virol. 2012 Oct;55(2):107-13. doi: 10.1016/j.jcv.2012.06.018. Epub 2012 Jul 20.


The impact of PCR-generated recombination on diversity estimation of mixed viral populations by deep sequencing.

Görzer I, Guelly C, Trajanoski S, Puchhammer-Stöckl E.

J Virol Methods. 2010 Oct;169(1):248-52. doi: 10.1016/j.jviromet.2010.07.040. Epub 2010 Aug 4.

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