Using HapFlow

If you'd like to explore a premade flow file one is available in the Example 1 zip file.

Quick start describes the workflow for using Hapflow with paired-end Illumina reads by creating a sorted BAM file and VCF file.

Tutorial 1 uses real data from mixed-strain infection of Koala. This tutorial will let you explore a premade flow file and show you how to separate reads into two operational taxonomic units.

Tutorial 2 covers the approach for generating BAM and VCF for read data containing three Chlamydia pecorum strains and visualizing the haplotypes with HapFlow