메뉴 건너뛰기




Volumn 31, Issue 1, 2015, Pages 94-101

VirVarSeq: A low-frequency virus variant detection pipeline for Illumina sequencing using adaptive base-calling accuracy filtering

Author keywords

[No Author keywords available]

Indexed keywords

HEPATITIS C VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 84922377591     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu587     Document Type: Article
Times cited : (41)

References (25)
  • 1
    • 84874964797 scopus 로고    scopus 로고
    • Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data
    • Beerenwinkel,N. et al. (2012) Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data. Front. Microbiol., 3, 329.
    • (2012) Front. Microbiol. , vol.3 , pp. 329
    • Beerenwinkel, N.1
  • 2
    • 81755185962 scopus 로고    scopus 로고
    • Ultra-deep sequencing for the analysis of viral populations
    • Beerenwinkel,N. and Zagordi,O. (2011) Ultra-deep sequencing for the analysis of viral populations. Curr. Opin. Virol., 1, 413-418.
    • (2011) Curr. Opin. Virol. , vol.1 , pp. 413-418
    • Beerenwinkel, N.1    Zagordi, O.2
  • 3
    • 79955943288 scopus 로고    scopus 로고
    • Added value of deep sequencing relative to population sequencing in heavily pre-treated HIV-1-infected subjects
    • Codoner,F.M. et al. (2011) Added value of deep sequencing relative to population sequencing in heavily pre-treated HIV-1-infected subjects. PLoS One, 6, e19461.
    • (2011) PLoS One. , vol.6 , pp. e19461
    • Codoner, F.M.1
  • 4
    • 84868687174 scopus 로고    scopus 로고
    • Improved base-calling and quality scores for 454 sequencing based on a Hurdle Poisson model
    • De Beuf,K. et al. (2012) Improved base-calling and quality scores for 454 sequencing based on a Hurdle Poisson model. BMC Bioinformatics, 13, 303.
    • (2012) BMC Bioinformatics. , vol.13 , pp. 303
    • De Beuf, K.1
  • 5
    • 84921810516 scopus 로고    scopus 로고
    • Deep sequencing of the HCV NS3/4A region confirms low prevalence of telaprevir-resistant variants both at baseline and end of study
    • Dierynck,I. et al. (2014) Deep sequencing of the HCV NS3/4A region confirms low prevalence of telaprevir-resistant variants both at baseline and end of study. J. Infect. Dis., 210, 1871-1880.
    • (2014) J. Infect. Dis. , vol.210 , pp. 1871-1880
    • Dierynck, I.1
  • 6
    • 52649157765 scopus 로고    scopus 로고
    • Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
    • Dohm,J.C. et al. (2008) Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res., 36, e105.
    • (2008) Nucleic Acids Res. , vol.36 , pp. e105
    • Dohm, J.C.1
  • 7
    • 84862579286 scopus 로고    scopus 로고
    • Viral quasispecies evolution
    • Domingo,E. et al. (2012) Viral quasispecies evolution. Microbiol. Mol. Biol. Rev., 76, 159-216.
    • (2012) Microbiol. Mol. Biol. Rev. , vol.76 , pp. 159-216
    • Domingo, E.1
  • 8
    • 0031978181 scopus 로고    scopus 로고
    • Base-calling of automated sequencer traces using phred
    • Ewing,B. and Green,P. (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res., 8, 186-194.
    • (1998) II. Error Probabilities. Genome Res. , vol.8 , pp. 186-194
    • Ewing, B.1    Green, P.2
  • 9
    • 77955690396 scopus 로고    scopus 로고
    • Minority variants of drug-resistant HIV
    • Gianella,S. et al. (2010)Minority variants of drug-resistant HIV. J. Infect. Dis., 202, 657-666.
    • (2010) J. Infect. Dis. , vol.202 , pp. 657-666
    • Gianella, S.1
  • 10
    • 84861214061 scopus 로고    scopus 로고
    • Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection
    • Henn,M.R. et al. (2012) Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection. PloS Pathog., 8, e1002529.
    • (2012) PloS Pathog. , vol.8 , pp. e1002529
    • Henn, M.R.1
  • 11
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows- Wheeler transform
    • Li,H. and Durbin,R. (2009) Fast and accurate short read alignment with Burrows- Wheeler transform. Bioinformatics, 25, 1754-1760.
    • (2009) Bioinformatics. , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 12
    • 84861108474 scopus 로고    scopus 로고
    • Highly sensitive and specific detection of rare variants in mixed viral populations from massively parallel sequence data
    • Macalalad,A.R. et al. (2012) Highly sensitive and specific detection of rare variants in mixed viral populations from massively parallel sequence data. PLoS Comput. Biol., 8, e1002417.
    • (2012) PLoS Comput. Biol. , vol.8 , pp. e1002417
    • Macalalad, A.R.1
  • 13
    • 0023783676 scopus 로고
    • Fitting mixture models to grouped and truncated data via the em algorithm
    • McLachlan,G.J. and Jones,P.N. (1988) Fitting mixture models to grouped and truncated data via the EM algorithm. Biometrics, 44, 571-578.
    • (1988) Biometrics. , vol.44 , pp. 571-578
    • McLachlan, G.J.1    Jones, P.N.2
  • 14
    • 80455126001 scopus 로고    scopus 로고
    • Evaluation of genomic high-throughput sequencing data generated on illumina HiSeq and genome analyzer systems
    • Minoche,A.E. et al. (2011) Evaluation of genomic high-throughput sequencing data generated on illumina HiSeq and genome analyzer systems. Genome Biol., 12, R112.
    • (2011) Genome Biol. , vol.12 , pp. R112
    • Minoche, A.E.1
  • 15
    • 79956314887 scopus 로고    scopus 로고
    • Genotype and SNP calling from next-generation sequencing data
    • Nielsen,R. et al. (2011) Genotype and SNP calling from next-generation sequencing data. Nat. Rev. Genet., 12, 443-451.
    • (2011) Nat. Rev. Genet. , vol.12 , pp. 443-451
    • Nielsen, R.1
  • 16
    • 84888997129 scopus 로고    scopus 로고
    • Stable HIV-1 integrase diversity during initial HIV-1 RNA decay suggests complete blockade of plasma HIV-1 replication by effective raltegravir-containing salvage therapy
    • Noguera-Julian,M. et al. (2013) Stable HIV-1 integrase diversity during initial HIV-1 RNA decay suggests complete blockade of plasma HIV-1 replication by effective raltegravir-containing salvage therapy. Virol. J., 10, 350.
    • (2013) Virol. J. , vol.10 , pp. 350
    • Noguera-Julian, M.1
  • 17
    • 85023630996 scopus 로고    scopus 로고
    • Genome-wide patterns of intrahuman dengue virus diversity reveal associations with Viral Phylogenetic Clade and Interhost Diversity
    • Parameswaran,P. et al. (2012) Genome-wide patterns of intrahuman dengue virus diversity reveal associations with Viral Phylogenetic Clade and Interhost Diversity. J. Virol., 93 (Pt 10), 2152-2157.
    • (2012) J. Virol. , vol.93 , pp. 2152-2157
    • Parameswaran, P.1
  • 18
    • 84885116145 scopus 로고    scopus 로고
    • Empirical validation of viral quasispecies assembly algorithms: State-of-The-art and challenges
    • Prosperi,M.C.F. et al. (2013) Empirical validation of viral quasispecies assembly algorithms: state-of-The-art and challenges. Sci. Rep., 3, 2837.
    • (2013) Sci. Rep. , vol.3 , pp. 2837
    • Prosperi, M.C.F.1
  • 19
    • 84862908315 scopus 로고    scopus 로고
    • Optimized filtering reduces the error rate in detecting genomic variants by short-read sequencing
    • Reumers,J. (2012) Optimized filtering reduces the error rate in detecting genomic variants by short-read sequencing. Nat. Biotechnol., 30, 61-68.
    • (2012) Nat. Biotechnol. , vol.30 , pp. 61-68
    • Reumers, J.1
  • 20
    • 84896520682 scopus 로고    scopus 로고
    • Antiviral therapy of hepatitis C in 2014: Do we need resistance testing
    • Schneider,M.D. et al. (2014) Antiviral therapy of hepatitis C in 2014: Do we need resistance testing? Antiviral Res., 105, 64-71.
    • (2014) Antiviral Res , vol.105 , pp. 64-71
    • Schneider, M.D.1
  • 21
    • 84900810127 scopus 로고    scopus 로고
    • Benchmarking of viral haplotype reconstruction programmes: An overview of the capacities and limitations of currently available programmes Brief
    • Shirmer,M. et al. (2014) Benchmarking of viral haplotype reconstruction programmes: an overview of the capacities and limitations of currently available programmes Brief. Bioinform., 15, 431-142.
    • (2014) Bioinform. , vol.15 , pp. 431-142
    • Shirmer, M.1
  • 22
    • 84922379596 scopus 로고    scopus 로고
    • Evaluating the use of the Illumina deep sequencing platform for the detection of minority variants in HIV and HCV
    • Manuscript under review
    • Thys,K. et al. (2014) Evaluating the use of the Illumina deep sequencing platform for the detection of minority variants in HIV and HCV. J. Virol. Methods, Manuscript under review.
    • (2014) J. Virol. Methods.
    • Thys, K.1
  • 23
    • 84900323186 scopus 로고    scopus 로고
    • Prevalence and evolution of low frequency HIV drug resistance mutations detected by ultra deep sequencing in patients experiencing first line antiretroviral therapy failure
    • Vandenhende et al. (2014) Prevalence and evolution of low frequency HIV drug resistance mutations detected by ultra deep sequencing in patients experiencing first line antiretroviral therapy failure. PLoS One, 9, p1.
    • (2014) PLoS One. , vol.9 , pp. p1
    • Vandenhende1
  • 24
    • 84871227763 scopus 로고    scopus 로고
    • LoFreq: A sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets
    • Wilm,A. et al. (2012) LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets. Nucleic Acids Res., 40, 11189-11201.
    • (2012) Nucleic Acids Res. , vol.40 , pp. 11189-11201
    • Wilm, A.1
  • 25
    • 79955125679 scopus 로고    scopus 로고
    • ShoRAH: Estimating the genetic diversity of a mixed sample from next-generation sequencing data
    • Zagordi,O. et al. (2011) ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data. BMC Bioinformatics, 12, 119.
    • (2011) BMC Bioinformatics. , vol.12 , pp. 119
    • Zagordi, O.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.