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Volumn 28, Issue 1, 2012, Pages 132-133

QuRe: Software for viral quasispecies reconstruction from next-generation sequencing data

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; CLASSIFICATION; CLUSTER ANALYSIS; COMPUTER PROGRAM; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; SEQUENCE ALIGNMENT; VIRUS; VIRUS GENOME;

EID: 84855173088     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr627     Document Type: Article
Times cited : (111)

References (21)
  • 1
    • 78651228163 scopus 로고    scopus 로고
    • The evolutionary analysis of emerging low frequency HIV-1 CXCR4 using variants through time-an ultra-deep approach
    • Archer, J. et al. (2010) The evolutionary analysis of emerging low frequency HIV-1 CXCR4 using variants through time-an ultra-deep approach. PLoS Comput. Biol., 6, e1001022.
    • (2010) PLoS Comput. Biol. , vol.6
    • Archer, J.1
  • 2
    • 79960878783 scopus 로고    scopus 로고
    • Inferring viral quasispecies spectra from 454 pyrosequencing reads
    • Astrovskaya, I. et al. (2011) Inferring viral quasispecies spectra from 454 pyrosequencing reads. BMC Bioinformatics, 12 (Suppl. 6), S1.
    • (2011) BMC Bioinformatics , vol.12 , Issue.SUPPL. 6
    • Astrovskaya, I.1
  • 3
    • 0034742452 scopus 로고    scopus 로고
    • Sequence alignment: an approximation law for the Z-value with applications to databank scanning
    • Bacro, J. N. and Comet, J. P. (2000) Sequence alignment: an approximation law for the Z-value with applications to databank scanning. Comput. Chem., 25, 401-410.
    • (2000) Comput. Chem. , vol.25 , pp. 401-410
    • Bacro, J.N.1    Comet, J.P.2
  • 4
    • 81755185962 scopus 로고    scopus 로고
    • Ultra-deep sequencing for the analysis of viral populations
    • doi:10.1016/j.coviro.2011.07.008
    • Beerenwinkel, N. and Zagordi, O. (2011) Ultra-deep sequencing for the analysis of viral populations. Curr. Opin. Virol.; doi:10.1016/j.coviro.2011.07.008.
    • (2011) Curr. Opin. Virol.
    • Beerenwinkel, N.1    Zagordi, O.2
  • 5
    • 44949250815 scopus 로고    scopus 로고
    • Viral population estimation using pyrosequencing
    • Eriksson, N. et al. (2008) Viral population estimation using pyrosequencing. PLoS Comput. Biol., 4, e1000074.
    • (2008) PLoS Comput. Biol. , vol.4
    • Eriksson, N.1
  • 6
    • 79956044149 scopus 로고    scopus 로고
    • Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing
    • Gilles, A. et al. (2011) Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing. BMC Genomics, 12, 245.
    • (2011) BMC Genomics , vol.12 , pp. 245
    • Gilles, A.1
  • 7
    • 0020484488 scopus 로고
    • An improved algorithm for matching biological sequences
    • Gotoh, O. (1982) An improved algorithm for matching biological sequences. J. Mol. Biol., 162, 705-708.
    • (1982) J. Mol. Biol. , vol.162 , pp. 705-708
    • Gotoh, O.1
  • 8
    • 77954383399 scopus 로고    scopus 로고
    • The RNA virus quasispecies: fact or fiction?
    • Holmes, E. C. (2010) The RNA virus quasispecies: fact or fiction? J. Mol. Biol., 400, 271-273.
    • (2010) J. Mol. Biol. , vol.400 , pp. 271-273
    • Holmes, E.C.1
  • 9
    • 40549123712 scopus 로고    scopus 로고
    • Population sequencing using short reads: HIV as a case study
    • Jojic, V. et al. (2008) Population sequencing using short reads: HIV as a case study. Pac. Symp. Biocomput., 13, 114-125.
    • (2008) Pac. Symp. Biocomput. , vol.13 , pp. 114-125
    • Jojic, V.1
  • 10
    • 79959309141 scopus 로고    scopus 로고
    • Deep sequencing of patient genomes for disease diagnosis: when will it become routine?
    • Kingsmore, S. F. and Saunders, C. J. (2011) Deep sequencing of patient genomes for disease diagnosis: when will it become routine? Sci. Transl. Med., 3, 87ps23.
    • (2011) Sci. Transl. Med. , vol.3
    • Kingsmore, S.F.1    Saunders, C.J.2
  • 11
    • 77950020240 scopus 로고    scopus 로고
    • Unfinished stories on viral quasispecies and Darwinian views of evolution
    • Más, A. et al. (2010) Unfinished stories on viral quasispecies and Darwinian views of evolution. J. Mol. Biol., 397, 865-877.
    • (2010) J. Mol. Biol. , vol.397 , pp. 865-877
    • Más, A.1
  • 12
    • 72849144434 scopus 로고    scopus 로고
    • Sequencing technologies - the next generation
    • Metzker, M. L. (2010) Sequencing technologies - the next generation. Nat. Rev. Genet, 11, 31-46.
    • (2010) Nat. Rev. Genet , vol.11 , pp. 31-46
    • Metzker, M.L.1
  • 13
    • 77952886150 scopus 로고    scopus 로고
    • Assembly algorithms for next-generation sequencing data
    • Miller, J. R. et al. (2010) Assembly algorithms for next-generation sequencing data. Genomics, 95, 315-327.
    • (2010) Genomics , vol.95 , pp. 315-327
    • Miller, J.R.1
  • 14
    • 80053628299 scopus 로고    scopus 로고
    • Sequencing technologies and genome sequencing
    • Pareek, C. S. et al. (2011) Sequencing technologies and genome sequencing. J. Appl. Genet., 52, 413-435.
    • (2011) J. Appl. Genet. , vol.52 , pp. 413-435
    • Pareek, C.S.1
  • 15
    • 84855174320 scopus 로고    scopus 로고
    • HIV-haplotype inference using a constraint-based dirichlet process mixture model
    • Machine Learning in Computational Biology (MLCB) workshop, Whistler, BC, Canada
    • Prabhakaran, S. et al. (2010) HIV-haplotype inference using a constraint-based dirichlet process mixture model. In Extended abstract at the Twenty-Third Annual Conference on Neural Information Processing Systems (NIPS), Machine Learning in Computational Biology (MLCB) workshop, Whistler, BC, Canada.
    • (2010) Extended abstract at the Twenty-Third Annual Conference on Neural Information Processing Systems (NIPS)
    • Prabhakaran, S.1
  • 16
    • 78650798688 scopus 로고    scopus 로고
    • Combinatorial analysis and algorithms for quasispecies reconstruction using next-generation sequencing
    • Prosperi, M. C. et al. (2011) Combinatorial analysis and algorithms for quasispecies reconstruction using next-generation sequencing. BMC Bioinformatics, 12, 5.
    • (2011) BMC Bioinformatics , vol.12 , pp. 5
    • Prosperi, M.C.1
  • 17
    • 34547643929 scopus 로고    scopus 로고
    • Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance
    • Wang, C. et al. (2007) Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance. Genome Res., 17, 1195-1201.
    • (2007) Genome Res , vol.17 , pp. 1195-1201
    • Wang, C.1
  • 18
    • 49949112775 scopus 로고    scopus 로고
    • HCV Quasispecies Assembly using Network Flows
    • Westbrooks, K. et al. (2008) HCV Quasispecies Assembly using Network Flows. Lect. Notes Comput. Sci., 4983, 159-170.
    • (2008) Lect. Notes Comput. Sci. , vol.4983 , pp. 159-170
    • Westbrooks, K.1
  • 19
    • 77950840976 scopus 로고    scopus 로고
    • Deep sequencing of a genetically heterogeneous sample: local haplotype reconstruction and read error correction
    • Zagordi, O. et al. (2010a) Deep sequencing of a genetically heterogeneous sample: local haplotype reconstruction and read error correction. J. Comput. Biol., 17, 417-428.
    • (2010) J. Comput. Biol. , vol.17 , pp. 417-428
    • Zagordi, O.1
  • 20
    • 78649901946 scopus 로고    scopus 로고
    • Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies
    • Zagordi, O. et al. (2010b) Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies. Nucleic Acids Res., 38, 7400-7409.
    • (2010) Nucleic Acids Res. , vol.38 , pp. 7400-7409
    • Zagordi, O.1
  • 21
    • 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


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