Benchmarking of viral haplotype reconstruction programmes: An overview of the capacities and limitations of currently available programmes

Briefings in Bioinformatics

Volumn 15, Issue 3, 2014, Pages 431-442

  Schirmer, Melanie ^a   Sloan, William T ^a   Quince, Christopher ^a  

^a UNIVERSITY OF GLASGOW   (United Kingdom)

Author keywords

Benchmarking; In silico data sets; Quasispecies; Statistics for validation; Viral haplotype reconstruction programmes

Indexed keywords

ANIMAL; BIOLOGY; COMPUTER PROGRAM; COMPUTER SIMULATION; FOOT AND MOUTH DISEASE VIRUS; GENETICS; HAPLOTYPE; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; MOLECULAR EVOLUTION; NUCLEIC ACID DATABASE; PROCEDURES; RNA VIRUS; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICS AND NUMERICAL DATA;

ANIMALS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DATABASES, NUCLEIC ACID; EVOLUTION, MOLECULAR; FOOT-AND-MOUTH DISEASE VIRUS; HAPLOTYPES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HIV-1; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; RNA VIRUSES; SOFTWARE;

EID: 84900810127     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbs081     Document Type: Article

References (22)

1. Ojosnegros O, Beerenwinkel N. Models of RNA virus evolution and their roles in vaccine design. Immunome Res 2010;6(Suppl 2):S5.
2. Bonhoeffer S, Nowak MA. Pre-existence and emergence of drug resistance in HIV-1 infection. ProcRSoc Lond B Biol Sci 1997;264(1382):631-7.
3. Glenn TC. Field guide to next-generation DNA sequencers. Mol Ecol Resour 2011;11(5):759-69.
4. Illumina. http://www.illumina.com/systems.ilmn (December 2012, date last accessed).
5. Yang Z, Goldman N, Friday A. Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation. Mol Biol Evol 1994;11(2):316-24.
6. Shimizu N, Okamoto T, Moriyama EN, et al. Patterns of nucleotide substitutions and implications for the immunological diversity of human immunodeficiency virus. FEBS Lett 1989;250(2):591-5.
7. Wright CF, Morelli MJ, Thebaud G, et al. Beyond the consensus: dissecting within-host viral population diversity of foot-and-mouth disease virus by using next-generation genome sequencing. JVirol 2011;85(5):2266-75.
8. Lee HY, Giorgi EE, Keele BF, et al. Modeling sequence evolution in acute HIV-1 infection. J Theor Biol 2009;261(2):341-60.
9. Nowak MA. What is a quasispecies? Trends Ecol Evol 1992;7(4):118-21.
10. Zagordi O, Bhattacharya A, Eriksson N, Beerenwinkel N. ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data. BMC Bioinformatics 2011;12(1):119.
11. Roth V. PredictHaplo. http://cs-wwwarchiv.cs.unibas.ch/personen/roth_volker/HivHaploTyper/index.html (December 2012, date last accessed).
12. Prabhakaran S, Rey M, Zagordi O, et al. HIV-haplotype inference using a constraint-based Dirichlet process mixture model. In: Machine Learning in Computational Biology (MLCB) NIPS Workshop 2010;1-4.
13. Prosperi MCF, Salemi M. QuRe: software for viral quasispecies reconstruction from next-generation sequencing data. Bioinformatics 2012;28(1):132-3.
14. Astrovskaya I, Tork B, Mangul S, et al. Inferring viral quasispecies spectra from 454 pyrosequencing reads. BMC Bioinformatics 2011;12(Suppl 6):S1.
15. Macalalad AR, Zody MC, Charlebois P, et al. Highly sensitive and specific detection of rare variants in mixed viral populations from massively parallel sequence data. PLoSComput Biol 2012;8(3):e1002417.
16. Henn MR, Boutwell CL, Charlebois P, et al. Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection. PLoS Pathog 2012;8(3):e1002529.
17. Zagordi O, Töpfer A, Prabhakaran S, et al. Probabilistic inference of viral quasispecies subject to recombination. In: RECOMB'12: Proceedings of the 16th Annual international conference on Research in Computational Molecular Biology. Berlin Springer, 2012;342-54.
18. Huang W, Li L, Myers JR, Marth GT. ART: a nextgeneration sequencing read simulator. Bioinformatics 2012;28(4):593-4.
19. Archer J, Baillie G, Watson SJ, et al. Analysis of high-depth sequence data for studying viral diversity: a comparison of next generation sequencing platforms using Segminator II. BMC Bioinformatics 2012;13(1):47.
20. Simen BB, Simons JF, Hullsiek KH, et al. Low-abundance drug-resistant viral variants in chronically HIV-infected, antiretroviral treatment-naive patients significantly impact treatment outcomes. J InfectDis 2009;199(5):693-701.
21. Le T, Chiarella J, Simen BB, et al. Low-abundance HIV drug-resistant viral variants in treatment-experienced persons correlate with historical antiretroviral use. PLoS ONE 2009;4(6):e6079.
22. Eriksson N, Pachter L, Mitsuya Y, et al. Viral population estimation using pyrosequencing. PLoS Comput Biol 2008;4(5):e1000074.