A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

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Anyone else having issues with tumor purity and ploidy assessments for ONT long read tools, I can't get the different tools to agree with each other.

I would sadly say the following: Welcome to copy number calling :sweat_smile:

Many times multiple solutions work, and then minor differences can result in roughly doubling/halving of ploidy solutions

I also have the WGS short-read for the same samples so that would be the ground truth?

short-read WGS will suffer the exact same issues as long-read based approaches (ASCAT for instance is developed initially for short read data)

FACS/karyotyping information would be a ground truth

Manual inspection of copy number profiles fit is what we typically do in our lab (if for example unrounded copy number profiles do not sit nicely on integer copy numbers, this indicates a bad fit)