Pf3k workflowΒΆ
Our main work flow consist with three steps:
- Use
dEploid
on clonal samples, and build a reference panel. - Use the IBD method to infer the proportions without a reference panel.
- Tune the haplotype with the given reference panel with fixed strain proportions
workflow
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
.