One way we made it fast was by mapping with simpleaf (github.com/COMBINE-lab/...) 🥳 This gives a ~50x speed-up over CellRanger, and natively produces spliced vs unspliced reads. Percent spliced reads is IMO *the* most important QC metric for single nuclei data (link.springer.com/article/10.1...).
A rust framework to make using alevin-fry even simpler - COMBINE-lab/simpleaf
