nomads-community/zambia-a724e-paper

Data and analysis for Pfkelch13 A724E detection in Zambia ## Data and analysis for *Pfkelch13* A724E detection in Zambia This repository contains the data and analysis code for the manuscript Mwenda et al. (2026) medRXiv. Sequencing data was analysed using Nomadic, which is publicly available here. Downstream analyses and figure generation was done in Jupyter Notebooks (see Repository overview). ## Repository overview The table below outlines the contents of the main folders of the repository: | Folder | Details | | -- | -- | | `day3data` | Day 3 positivity data from the clinical study Kaoma. | | `ic50data` | IC50 data from *ex vivo* analysis of samples from the clinical study in Kaoma. | | `metadata` | Sample metadata for cross-sectional studies. | | `microsatdata` | Flanking microsatellite data and analysis code for A724E carrying isolates. | | `sangerdata` | Sanger sequencing data anad analysis code confirmation of A724E by two assays. | | `scripts` | Scripts to run `nomadic summarize` for processing and view sequencing data dashboard. | | `seqdata` | Sequencing data for cross-sectional and longitudinal studies. | | `notebooks` | Jupyter Notebooks containing manuscript analyses. | | `figures` | Figures for the manuscript; generated by running `notebooks`. | | `tables` | Tables for the manuscript; generated by running `notebooks.` | ## Sequencing data Sequencing data is available in the `seqdata` folder. The `all` folder contains data from the cross-sectional studies and archival sample sequencing; the `exvivo` folder contains sequencing data from the clinical study in Kaoma. Within each, you can find the following folders: | Folder | Details | | -- | -- | | `results` | Folders for all sequencing experiments. | | `results/ ` | Nomadic outputs for an individual sequencing experiment called ` `. | | `results/ /summary.variants.csv` | CSV file containing filtered and annotated variant calls for *Pfkelch13* and *ama1* for the experiment. | | `results/ /vcfs/summary.variants.vcf.gz` | VCF file containing all *Pfkelch13* and …