slide_snake is a [Snakemake](https://snakemake.readthedocs.io/en/stable/) workflow for preprocessing, alignment, and quantification of spatial RNA-sequencing data, designed to work for any commercial or custom platform. Specifically, we aim to support custom workflows for which existing pipelines don’t quite cut it - starting with total RNA data.

Getting Started:

Pipeline Details:

Reference:

Indices and tables