Bioinformatics Pipeline

Streamlined spatial sequencing
data analysis

The Curio Seeker bioinformatics pipeline enables quick and easy data analysis from Curio Seeker Spatial Mapping Kits.

Pipeline Workflow

The Curio Seeker bioinformatics pipeline processes FASTQ files generated from Curio Seeker sequencing libraries into spatial gene expression maps in a single, efficient package. The pipeline also provides quality control and preliminary cluster and spatial variable gene analyses in a simple .html report for initial data interpretation of the Curio Seeker experiment.

Pipeline output is compatible
with third party analysis and visualization tools

Gene-by-bead matrices and spatial coordinates from the pipeline are provided in data formats (.rds, .h5ad, and .mtx) that are compatible with many spatial transcriptomic and single-cell analysis packages published in R and python.

Examples include NAPARI, Cell2location, RCTD, C-Side, Seurat, Scanpy, and Squidpy. The single-cell scale resolution nature of Curio Seeker data also enables visualization of the output with various single cell data browsers.

Cell type annotation by RCTD

Two flexible options for pipeline access

The pipeline can be installed and deployed locally or accessed via our bioinformatics portal, each catering to different needs.

Local installation

Cloud analysis

Contact sales for more information.

Please refer to the knowledge base for more information on downloading and running the pipeline at your institution or for utilizing our cloud-based version of the bioinformatics pipeline. Additional questions can be directed to technical support.

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Explore Curio Seeker documentation

Read details of the Curio Seeker kits

Access an overview of the Curio Seeker technology

See the kind of data you can uncover with Curio Seeker kits