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References
Publications reporting the ANGSD program, detailing the methods used in ANGSD, or testing the accuracy of ANGSD relative to other approaches.
###The paper reporting the ANGSD program:
Korneliussen T, Albrechtsen A, Nielsen R (2014) ANGSD: Analysis of Next Generation Sequencing Data. BMC Bioinformatics 15: 356.
###The paper reporting the ANGSD-wrapper program:
Durvasula A, Hoffman PJ, Kent TV, Liu C, Kono TJY, Morrell PL, Ross-Ibarra J (2016) ANGSD-wrapper: utilities for analyzing next generation sequencing data. Mol Ecol Resour.
###Methods used in ANGSD are explained in:
Nielsen R, Korneliussen T, Albrechtsen A, Li Y, Wang J (2012) SNP calling, genotype calling, and sample allele frequency estimation from New-Generation Sequencing data. PLoS One 7: e37558.
###FST and PCA methods are detailed in:
Fumagalli M, Vieira FG, Korneliussen TS, Linderoth T, Huerta-Sanchez E, Albrechtsen A, Nielsen R (2013) Quantifying population genetic differentiation from next-generation sequencing data. Genetics 195: 979-992.
###Estimation of individual inbreeding coefficients are detailed in:
Vieira FG, Fumagalli M, Albrechtsen A, Nielsen R (2013) Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation. Genome Res 23: 1852-1861.
###A comparison of the accuracy of population genetic analyses using ANGSD versus various SNP calling approaches:
Han E, Sinsheimer JS, Novembre J (2014) Characterizing bias in population genetic inferences from low-coverage sequencing data. Mol Biol Evol 31: 723-735.
###ANGSD-related papers
Durvasula A, Kent TV, Hoffman PJ, Liu C, Kono TJY, Morrell PL, Ross-Ibarra J (2015) ANGSD-wrapper. PeerJ PrePrints 3: e1837.
Korneliussen TS, Moltke I (2015) NgsRelate: a software tool for estimating pairwise relatedness from next-generation sequencing data. Bioinformatics 31: 4009-4011.
Vieira FG, Lassalle F, Korneliussen TS, Fumagalli M (2015) Improving the estimation of genetic distances from Next Generation Sequencing data. Biol J Linn Soc 117: 139-149.