Cidder secondary clustering

[jsgounot]

Hi,

thanks for your tools. I was wondering if you could implement a second clustering approach for Cidder as well, similar to the --determine-clusters option on Skder.

Thanks!
JS

[raufs]

Thank you for the suggestion! Yes, of course, should be straightforward, will work on it for the next release.

Rauf

[raufs]

@jsgounot Sorry for the delay, NCBI's GenBank database has been down this week and so was waiting on it to be back up to further test, but seems to work well on the test dataset and have added both a secondary clustering to find the best matching reference genome(s) for a focal genome based both on protein cluster containment (-n) or alternatively via skani ANI (-ns).

Also, I shifted the arguments a little with this latest release.

Version just released and should be on bioconda later today.

[jsgounot]

Hey @raufs, thanks for the update! I'll try this out soon.