The goal is to provide a lot of flexibility in a familiar framework, while delivering robust analysis methods coupled with extensive visualization options.

Check it out!

github.com/lrylaarsdam/...

Huge thanks to all co-authors and the inimitable @jbuenrostro.bsky.social for supporting this new direction - I got to think about evolution, engineering, chromatin biophysics, and modeling during the course of this project. For more, check out the preprint: www.biorxiv.org/content/10.1... 8/9

Thanks for this! What is your take when sample quality means only modest ATAC-seq quality is possible. (too low is not usable, so let's say borderline) In many cases, eg primary tumors etc... high quality can never be achieved. What is the threshold for different analyses that can be performed?

2) HyDrop-v2: with a new bead design it provides scalable and cost-effective generation of scATAC-seq atlases. With HyDrop atlases of the fly embryo and mouse cortex we show that CREsted models trained on HyDrop data are equivalent to models trained 10x atlases. www.biorxiv.org/content/10.1...

"Single" cell... no editing typos on bluesky I guess.

Finally, we leverage stepwise, indexed tagmentation to produce ATAC and DNA methylation profiles from the same cells. We believe this will be particularly useful for bridging to ATAC atlases to better facilitate Cell type annotation.

To enable more sequencing options, we also developed primers for direct preparation for sequencing on Ultima Genomics instruments. We sequenced >140k cells from human cortex.

We also show you can use enzymatic conversion methods instead of bisulfite.

The core of the improvement is an additional layer of indexing. This is done while maintaining the same molecular structure as sciMETv2 which enables compatibility with our sciMET-CAP capture workflow. (genomebiology.biomedcentral.com/articles/10....)