Analytic optimization of Plasmodium falciparum marker gene haplotype recovery from amplicon deep sequencing of complex mixtures

Data, code, and figures related to the manuscript "Analytic optimization of Plasmodium falciparum marker gene haplotype recovery from amplicon deep sequencing of complex mixtures"

Contained in this directory are:

1. haplotype_recovery_experiment.Rmd: The R Markdown file that enables recreation of all tables, numbers, and figures contained in the manuscript.
2. haplotype_recovery_experiment.html: The rendered R Markdown file in html format.
3. data folder: data files used in haplotype_recovery_experiment.Rmd. See README.md in the data folder for more information.
4. figures folder: the figures present in the manuscript, generated by running haplotype_recovery_experiment.Rmd.