Introduction

NovaScope is a sophisticated pipeline containing multiple steps for processing spatial transcriptomics data. Installing individual software tools and setting up the pipeline for your specific environment requires a detailed understanding of your computational environment as well as the overall structure of the NovaScope pipeline.

In this short tutorial, we will use the Docker and Singularity containers to facilitate the installation and execution of the NovaScope pipeline with minimal test examples. These examples will give you a basic understanding of the pipeline with minimal effort.

However, to take full advantage of various features offered by the NovaScope pipeline, such as systematic parallelization in HPC environment with SLURM, we strongly recommend that you install the pipeline in your computing environment rather than relying solely on the pre-built Docker image. Please refer to the Installation Guide for detailed instructions on how to install the pipeline in your computing environment. The Basic Usage and Full Documentation sections provide more detailed instructions on how to run the pipeline with your own data and computing environment.