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 preprint at DOI: 10.1101/2024.03.29.587285.
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.
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
The Full Documentation serves as a comprehensive overview of NovaScope's functionality, featuring:
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.