batch correction strategies

[wangjiawen2013]

Hi,
Harmony and MNNCorrect were used for batch correction in multi-sample pipeline (https://kzhang.org/SnapATAC2/tutorials/integration.html)，Can I use scvi-tools to integrate samples ? And I found that scvi-tools and scanvi was used for cluster annotation, why don't you use them in multi-sample pipeline ?

[kaizhang]

Harmony and MNNCorrect work as a post-preprocessing step of SnapATAC2's dimension reduction algorithm, while scvi-tools works on the raw counts. These are two different strategies. If you use scvi-tools or PeakVI, then SnapATAC2 is not needed.