Citation

If you publish research that uses ngstools you have to cite it as follows:

ngsTools package can be cited as:

  • Fumagalli, M., Vieira, F. G., Linderoth, T., & Nielsen, R. (2014). ngsTools: methods for population genetics analyses from next-generation sequencing data. Bioinformatics, 30(10), 1486–1487. https://doi.org/10.1093/bioinformatics/btu041

ANGSD can be cited as:

  • Korneliussen, T., Albrechtsen, A., & Nielsen, R. (2014). ANGSD: Analysis of Next Generation Sequencing Data. BMC Bioinformatics, 15(1), 356. https://doi.org/10.1186/s12859-014-0356-4
  • 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(7), e37558. https://doi.org/10.1371/journal.pone.0037558

FST and PCA methods can be cited as:

  • Fumagalli, M., Vieira, F. G., Korneliussen, T. S., Linderoth, T., Huerta-Sánchez, E., Albrechtsen, A., & Nielsen, R. (2013). Quantifying Population Genetic Differentiation from Next-Generation Sequencing Data. Genetics, 195(3), 979–992. https://doi.org/10.1534/genetics.113.154740

Inbreeding estimation can be cited as:

  • Vieira, F. G., Fumagalli, M., Albrechtsen, A., & Nielsen, R. (2013). Estimating inbreeding coefficients from NGS data: impact on genotype calling and allele frequency estimation. Genome Research, 23(11), 1852–1861. https://doi.org/10.1101/gr.157388.113
  • Vieira, F. G., Albrechtsen, A., & Nielsen, R. (2016). Estimating IBD tracts from low coverage NGS data. Bioinformatics, 32(13), 2096–2102. https://doi.org/10.1093/bioinformatics/btw142

Nucleotide diversity estimates from NGS data implemented here have been proposed in:

  • Yi, X., Liang, Y., Huerta-Sanchez, E., Jin, X., Cuo, Z. X., Pool, J. E., Xu, X., Jiang, H., Vinckenbosch, N., Korneliussen, T. S., Zheng, H., Liu, T., He, W., Li, K., Luo, R., Nie, X., Wu, H., Zhao, M., Cao, H., ... Wang, J. (2010). Sequencing of 50 human exomes reveals adaptation to high altitude. Science, 329(5987), 75–78. https://doi.org/10.1126/science.1190371
  • Korneliussen, T. S., Moltke, I., Albrechtsen, A., & Nielsen, R. (2013). Calculation of Tajima's D and other neutrality test statistics from low depth next-generation sequencing data. BMC Bioinformatics, 14(289). https://doi.org/10.1186/1471-2105-14-289
  • Fumagalli, M. (2013). Assessing the effect of sequencing depth and sample size in population genetics inferences. PLoS ONE, 8(11), e79667. https://doi.org/10.1371/journal.pone.0079667

Estimation of genetic distances have been described here:

Vieira, F. G., Lassalle, F., Korneliussen, T. S., & Fumagalli, M. (2016). Improving the estimation of genetic distances from next-generation sequencing data. Biological Journal of the Linnean Society, 117(1), 139–149. https://doi.org/10.1111/bij.12511