single cell sequencing data doublets removal tools selection

Question

[shoujun.gu]

Based on my search, I found there are 3 major tools for removal of doublets from single cell sequencing:

1. Scrublet

2. DoubletDecon

3. DoubletFinder

.I'd like to know what's the major difference of these tools? Which one performs better?

Thanks.

[psm]

I'm also interested in this question 1 year later... Anyone have any experience with any of these tools or assessed how well they perform?

Thanks in advance.

Answer 1

[predeus]

There's a new and quite comprehensive benchmark paper.

They compare about 8 tools I think, coming to a conclusion that scrublet and DoubletFinder perform quite well.

In my own experience, DoubletFinder takes quite a long time and also requires more memory (50 Gb for a 10k cells dataset). I also suspect it's prone to removing rare clusters - I'm looking into the issue right now, but in my test dataset (namely, 10k PBMC cells from 10X) it removed all dendritic cells.

So, despite it performing well in the benchmark, I'd recommend caution.