This workspace contains workflows for processing Plasmodium amplicon sequencing data using Illumina platforms in the Terra platform. It is panel-agnostic and includes two main workflows:
- 01_Illumina_Amplicon_Processing: Preprocesses raw reads, removes sequencing errors (denoising), and prepares data for genotyping.
- 02_Plasmodium_Genotype_Population_Analysis: Performs genotype analysis and produces summary reports, including frequency maps of drug resistance.
Reference data and example datasets for multiple panels (e.g. MAD4HatTeR, AMPLseq, SIMPLseq) are included.
📬 Contact: [email protected]