scprocess is a Snakemake pipeline designed to streamline and automate processing of single cell RNA sequencing data. Optimized for data generated using the 10x Genomics technology, it provides a comprehensive solution that transforms raw sequencing files into standardized outputs suitable for a variety of downstream tasks. The pipeline is built to support the analysis of datasets comprising multiple (i.e. 100+) samples via a simple CLI.
For detailed setup instructions, extended reference guides, and step-by-step tutorials on example datasets, please visit:
👉 https://marusakod.github.io/scprocess/
scprocess consists of a series of core steps which can be performed in a single execution of the workflow. Additional steps are available to extend the core analyses as needed.
Overview of scprocess including input file requirements, all pipeline steps and specific software packages/algorithms used.