Welcome to NovaScope documentation

Introduction

NovaScope is a Snakemake-based pipeline that processes spatial transcriptomics data generated from the Seq-Scope. Currently, it is tailored to process the spatial arrays generated from the Illumina NovaSeq 6000 platform. The preprint for NovaScope is available at DOI: 10.1101/2024.03.29.587285.

Functionality

The main purpose of NovaScope is to process raw sequencing data (1st-seq and 2nd-seq), align reads to the reference genome, and produce spatial gene expression at the submicron resolution.

It provides additional functionalities for accurate histological images alignment with transcriptome dataset, conversion of spatial gene expression data for compatibility with FICTURE, and the organization of pixels into customizable hexagonal grids.

It features a modular and adaptable design, enabling users to tailor the pipeline according to their particular requirements.

Infrastructure

This pipeline is built to operate on Unix-based high-performance computing (HPC) platforms, with the capability to run either directly on local systems or via the Slurm workload manager.

Overview

NovaScope primarily consists of two steps as shown in the figure below.

Figure 1: Overview of the NovaScope pipeline: Step 1 processes the 1st-seq FASTQ files to generate spatial barcode maps for each "Chip", a 10x6 array of tiles. Step 2 processes the 2nd-seq FASTQ files, aligns reads to the reference genome, and produces spatial gene expression at submicron resolution.