Pf3k workflowΒΆ

Our main work flow consist with three steps:

  1. Use dEploid on clonal samples, and build a reference panel.
  2. Use the IBD method to infer the proportions without a reference panel.
  3. Tune the haplotype with the given reference panel with fixed strain proportions

Pf3k workflowworkflow

Black boxes indicate the key deconvolution steps when our program DEploid is used. Boxes in blue and purple represent the input and output respectively at each step. Steps Deconvolution with IBD and Deconvolution with a reference panel can be combined by using the flag -ibd.