Compare trees generated by mixed technology, with that from illumina/compass

mbhall88 / head_to_head_pipeline

Snakemake pipelines to run the analysis for the Illumina vs. Nanopore comparison.

GNU General Public License v3.0

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Compare trees generated by mixed technology, with that from illumina/compass #71

Closed iqbal-lab closed 2 years ago

iqbal-lab commented 3 years ago

I think this is a nice idea (given our SNP distances are so close), but i recall that our nanopore SNP distances are only very close to illumina ones when you zoom in to small distances. So i propose we do not do this.

However, future reference, take a look at the section on quantifying differences between trees here https://wellcomeopenresearch.org/articles/3-33/v1

They use

the Kendall-Colijn metric to see if the topology is correct, ignoring branch lengths
looking at BAPs clusters

iqbal-lab commented 3 years ago

As i said, am happy to close this