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This study assessed the spatial genetic variation in P. falciparum populations in Mali

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P. falciparum population genetic in MALI

This repository holds all data and plotting scripts needed to reproduce plots from the paper "Genome-wide SNP analysis of Plasmodium falciparum show differentiation at drug resistance associated loci between malaria transmission settings in Southern Mali", by A. Coulibaly, M.F. Diop and A. Amambua-Ngwa et. al. This includes plots in the main text and in the supplemental material. In cases where the plotting data and scripts are located elsewhere, the relevant links are contained within the figure folder.

Dependencies

The following need to be installed and in the path...

  • R (v4.0.3 (2020-10-10))
    • adegenet
    • ggplot2
    • cowplot (v1.1.1)
    • dplyr (v1.0.9)
    • fdrtool
    • finepop
    • mmod
    • moimix
    • PopGenome (v2.7.5)
    • patchwork (v1.1.1)
    • pophelper (v2.3.1)
    • rehh (v3.2.2)
    • SNPRelate (v1.30.0)
    • tess3r (v0.5.0)
    • tidyverse (v1.3.2)
    • LDheatmap
  • Rstudio
  • ADMIXTURE (v1.3.0)
  • vcflib (v1.0.3)
  • plink (v2.0)
  • bcftools (v1.9)
  • vcftools (v0.1.17)

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This study assessed the spatial genetic variation in P. falciparum populations in Mali

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