Fig. 2

Schematic overview of a WASP analysis. As a first step, users start the Snakemake workflow on a Linux-based system, providing the FASTQ file with the reads and a reference genome with corresponding annotation. The results (quality metrics) of the workflow are then presented in an R Shiny web application which generates a gene expression matrix CSV file containing UMIs per gene and cell. This file or a similar externally generated file are then uploaded to the post-processing Shiny web application for further processing. Post-processing can be performed in an automated or manual mode and presented as a dynamic web page similar to the pre-processing results