vivaxGEN Microhaplotypes Pipeline Documentation

VivaxGEN-Microhaps is an open-source pipeline designed for processing targeted amplicon sequencing data. It offers two distinct sub-pipelines:

• Microhaplotype Calling: This sub-pipeline, adapted from the malaria-amplicon-pipeline and converted to use Snakemake, generates microhaplotype allele tables.

• SNP-based Variant Calling: Leveraging the vivaxGEN NGS-Pipeline, this sub-pipeline generates standard VCF files for SNP analysis. The main documentation for vivaxGEN NGS-Pipeline is here.

User Documentation

• Installation on local devices and HPCs
  • Updating the pipeline
• Introduction to DADA2-based MicroHaplotype Analysis
  • Quick Start
• Introduction to SNP-based variant calling
  • Quick Start

Developer Documentation

• Implementing microhaplotypes calling for different panel
  • Configuration Files
  • Reference Files