mfdiop/gambia-malaria-connectivity

Resolve the source of residual Plasmodium falciparum transmission in western Gambia, using whole-genome parasite connectivity. # Gambia malaria connectivity — Importation versus local transmission PhD analysis (Objective 3) resolving the source of residual *Plasmodium falciparum* transmission in western Gambia, using whole-genome parasite connectivity. We ask whether residual malaria in low-prevalence western regions is sustained by **local transmission**, **importation from the higher-transmission eastern Gambia**, or **cross-border importation from Senegal**, and whether that balance is shifting as The Gambia approaches elimination. This work extends Amambua-Ngwa et al. (2019) — which used 54-SNP barcodes to detect 60 directional transmission events — into WGS resolution, removing four constraints simultaneously: barcode resolution, p-distance recombination artefacts, polyclonal infections, and absence of Senegalese comparators. ## Project structure ``` codes/ # Analysis scripts (phase-based + exploratory variants) phase1_01_wgs_qc.R phase1_02_coi_stratification.R phase1_03_sample_annotation.R phase2_01_fst_ibd_mantel.R phase2_02_pca_admixture.R phase2_02_pca_lea.R phase2_02_pca_lea_extendK.R phase2_03_hmmibd.R phase3_01_supervised_admixture.R phase3_02_directional_ibd.R phase3_03_isolation.R clustering_approaches.R clustering_approaches_v1.R data/ # Primary genomics inputs and metadata gambia.vcf senegam_pf.vcf gambia_2014isolates/ metadata/ notes/ # Study plan and modelling notes objective3_proposal.md objective3_proposal.docx directional_connectivity_Amambua-Ngwamodel.md results/ # Script outputs organized by phase phase1_01/ phase1_02/ phase1_03/ phase2_01/ phase2_02_lea/ phase2_03/ phase3_01/ phase3_02/ phase3_03/ phase4_01/ tools/ hmmIBD/ # Local helper assets/utilities for hmmIBD workflows gambia-malaria-connectivity.Rproj # RStudio project entry point CLAUDE.md # Local coding- …