How to infer reliable diploid genotypes from NGS or traditional sequence data: from basic probability to experimental optimization
Article first published online: 16 MAR 2012
© 2012 The Author. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology
Journal of Evolutionary Biology
Volume 25, Issue 5, pages 949–960, May 2012
How to Cite
CHENUIL, A. (2012), How to infer reliable diploid genotypes from NGS or traditional sequence data: from basic probability to experimental optimization. Journal of Evolutionary Biology, 25: 949–960. doi: 10.1111/j.1420-9101.2012.02488.x
- Issue published online: 5 APR 2012
- Article first published online: 16 MAR 2012
- Received 8 September 2011; revised 6 February 2012; accepted 7 February 2012
- 1763. An essay towards solving a problem in the doctrine of chances. By the late Rev. Mr Bayes, F.R.S. communicated by Mr Price, in a letter to John Canton A.M.F.R.S. Phil. Trans. 53: 370–418. &
- 2009. High-resolution, high-throughput HLA genotyping by next-generation sequencing. Tissue Antigens 74: 393–403. , , , , , et al.
- 1975. A method for combining non-independent, one-sided tests of significance. Biometrics 31: 987–992.
- 2006. Choosing the right Molecular Genetic Markers for studying biodiversity: from molecular evolution to practical aspects. Genetica 127: 101–120.
- 2010. An efficient method to find potentially universal population genetic markers, applied to metazoans. BMC Evol. Biol. 10: 276. , , , , , et al.
- 2009. OLFinder:a program which disentangles DNA sequences containing heterozygous indels. Mol. Ecol. Res. 10: 335–340.
- 2011. Histoire évolutive, structures génétique, morphologique et écologique comparées dans un complexe d’espèces jumelles: Echinocardium cordatum (Echinoidea, Irregularia). PhD thesis, 321 pp. Aix-Marseille université, Marseille.
- 2011. Applications of next generation sequencing in molecular ecology of non-model organisms. Heredity 107: 1–15. &
- 2007. Evidence for a slightly deleterious effect of intron polymorphisms at the EF1 alpha gene in the deep-sea hydrothermal vent bivalve Bathymodiolus. Gene 406: 99–107. , , , &
- 2010. A 454 multiplex sequencing method for rapid and reliable genotyping of highly polymorphic genes in large-scale studies. BMC Genomics 11: 296. , , , &
- 2010. Nuclear gene phylogeography using PHASE: dealing with unresolved genotypes, lost alleles, and systematic bias in parameter estimation. BMC Evol. Biol. 10: 118. , &
- 2010. Bayesian analysis of molecular variance in pyrosequences quantifies population genetic structure across the genome of Lycaeides butterflies. Mol. Ecol. 19: 2455–2473. , , , , &
- 2009. High-throughput genotyping by whole-genome resequencing. Genome Res. 19: 1068–1076. , , , , , et al.
- 2009. Estimation of allele frequencies from high-coverage genome-sequencing projects. Genetics 182: 295–301.
- 2011. Identification and correction of systematic error in high-throughput sequence data. BMC Bioinformatics 12: 451. , , , , &
- 2011. Genotype and SNP calling from next-generation sequencing data. Nat. Rev. Genet. 12: 443–451. , , &
- 2011. Technology-specific error signatures in the 1000 Genomes Project data. Hum. Genet. 130: 505–516. , , , , , et al.
- 2003. A comparison of Bayesian methods for haplotype reconstruction from population genotype data. Am. J. Hum. Genet. 73: 1162–1169. &
- 2000. SSCP is not so difficult: the application and utility of single-stranded conformation polymorphism in evolutionary biology and molecular ecology. Mol. Ecol. 9: 1699–1710. , , , , &
- 1998. Short allele dominance as a source of heterozygote deficiency at microsatellite loci: experimental evidence at the dinucleotide locus Gv1CT in Gracilaria gracilis (Rhodophyta). Mol. Ecol. 7: 1569–1573. , , &