Analyses for the manuscript "Prevalence of molecular markers of antimalarial drug resistance across altitudinal transmission zones in highland western Uganda" by Ross Boyce, Nicholas F. Brazeau, Travis Fulton, Nick Hathaway, Michael Matte, Moses Ntaro, Edgar Mulogo, Jonathan J. Juliano (PMID: 31436149)

All commands to run SeekDeep v2.6.0 are in the SeekDeep Directory within the uganda_seekdeep.py snakemake file. Sample names, molecular identification barcodes, primers and pools are listed within the text files.

All statistical analysis are in the R Directory and are contained with the markdown files: Uganda_DrugRx_NFB_v3.Rmd. The Uganda_DrugRx_NFB_v3.Rmd calls NFBtools, which is a personal suite of functions located here.