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RasmussenLab / phamb

Downstream processing of VAMB binning for Viral Elucidation
MIT License
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VAE or AAE? #57

Closed yqy6611 closed 9 months ago

yqy6611 commented 9 months ago

Hi all, I'd like to learn which cluster file generated by vamb is suitable for feeding to phamb, that via VAE or AAE. Many thanks!

joacjo commented 9 months ago

Hi Qiyi Yuan

We have only benchmarked using the clusters from the VAE model to phamb, so I would advise to you that one. However, you can make your own small benchmark to learn if there is a benefit to use the AAE derived clusters on your data by evaluating the number of HQ vMAGs you achieve from using either one.