Implementing avamb workflow

[johnne]

Hi,
I like the addition of vamb as a binner. Have you seen the Avamb Snakemake workflow by the vamb developers? I wonder if it's something you plan on implementing in atlas?

Thanks for a nice tool!

[SilasK]

What exactly is the difference between vamb and avamb?

[johnne]

Main difference seems to be the type of "encoder" used in the neural network. I admit the underlying method is too technical for me to grasp fully, but while the original vamb uses a "variational autoencoder", the new binner (called AAMB) uses an "adversarial autoencoder" (see the biorxiv paper here) which the authors claim perform even better than vamb. The Avamb workflow combines both tools in order to generate better bins compared to running each tool separately.

[SilasK]

I looked at it and the workflow seems not so straight forward to copy. Have you tried it?