Overview

The DRAGEN StrataMap analysis software processes spatial sequencing data along with the registered microscope image. It aligns sequencing reads to their respective spatial locations and organizes them into square grids and individual cells, using H&E image processing for cell identification. The software performs filtering, normalization, dimensionality reduction, and clustering. The resulting spatial data can be explored using the Illumina Connected Multiomics (ICM) spatial data viewer for deeper insights and interaction.

Illumina Connected Analytics Pipeline

DRAGEN Spatial Transcriptome is available in the cloud as a hosted application on the Illumina BioInsight Platform Core (Core). The Cloud App is designed for customers aiming to harness cloud computing capabilities for high performance analysis of sequencing data seamlessly integrated with the Illumina Connected Multiomics platform.

DRAGEN App Manager Application

DRAGEN StrataMap is available locally through the use of the DRAGEN App Manager (DAM) platform which can be installed onto a locally managed DRAGEN Server. The Local App is designed for customers who require an on‑premises option for running analyses on their DRAGEN server. It provides a streamlined workflow that allows users to perform analysis without relying on external cloud services.

The local DAM App does not include the tertiary steps available in the cloud app (filtering, normalization, PCA, UMAP, clustering). Those steps can be run on the data imported into ICM.

In order to enable checking cell segmentation before sequencing, the cell segmentation portion of the pipeline is available as a standalone tool, see Illumina StrataMap Cell Segmentation Tool.