NovaScope

NovaScope is a Snakemake-based pipeline designed for processing spatial transcriptomics data generated from Seq-Scope. Currently, it is optimized for handling spatial arrays produced by the Illumina NovaSeq 6000 platform.

For a detailed tutorial, please visit NovaScope Tutorial.

You can find the protocol paper at DOI : 10.1038/s41596-024-01065-0.

Installation

To install and set up NovaScope, please follow these steps:

• Refer to this guide to install NovaScope, Snakemake, and other required software, and to download the reference database.
• Follow this guide to set up an environment configuration file.
• If you are an HPC user preferring to use SLURM for job management, please check this guide to configure a job management profile.

Examples and Basic Usage

We provide three examples in the testrun folder, complete with concise instructions, including:

• Accessing Example Datasets
• Configuring a NovaScope Run
• Executing the NovaScope Pipeline
• Understanding the Output

Full Documentation

The Full Documentation serves as a comprehensive overview of NovaScope's functionality, featuring:

• A Rule Execution Guide
• A Detailed Instruction for Each Rule

Exemplary Downstream Analysis

For the spatial digital gene expression matrix created by NovaScope, we provide an exemplary downstream analysis at NovaScope-exemplary-downstream-analysis (NEDA). NEDA demonstrates (1) how to identify spatial factors at a pixel-level resolution and (2) how to identify cell-type clusters by aggregating the SGE matrix at the cellular level according to histology files.