nf-core pipeline · 10x-genomics, 10xgenomics, image-processing
nf-core/spatialvi
A Nextflow pipeline for processing and analysing 10x Genomics Visium spatial transcriptomics data.
What nf-core/spatialvi is
nf-core/spatialvi is a bioinformatics analysis pipeline designed for spatially resolved transcriptomics. It processes gene count data in combination with spatial coordinates and microscopy tissue images, specifically catering to the 10x Genomics Visium platform.
Originally established at the Jackson Laboratory, the pipeline was developed further through a collaboration between the National Bioinformatics Infrastructure Sweden and the National Genomics Infrastructure at SciLifeLab. It provides a standard workflow for researchers working with Visium data, supporting workflows initiated from raw sequence data or pre-computed outputs.
What the pipeline does
The workflow is implemented in Nextflow DSL2 and executes tasks inside isolated Docker or Singularity software containers, with single-container allocations per process drawn from nf-core modules. Users specify inputs such as sequencing reads, tissue images, or pre-computed files using a structured samplesheet.
The pipeline either triggers 10x Genomics Space Ranger to process raw datasets or ingests data already processed by Space Ranger. It then handles the integration and analysis of spatially resolved gene counts alongside coordinate data and tissue histology images.
Key facts
- Pipeline engine
- Nextflow DSL2
- Target platform
- 10x Genomics Visium
- Input formats
- Samplesheet CSV with raw spatial data or pre-processed Space Ranger outputs
- Containerisation
- Docker, Singularity
- Primary maintainers
- Erik Fasterius and Christophe Avenel
- Originating organisation
- The Jackson Laboratory
What you can use it for
- Primary Visium data processing
- Processing raw sequencing data and microscopy images from 10x Genomics Visium assays by running Space Ranger within the pipeline.
- Post-Space Ranger spatial analysis
- Analysing spatial gene expression matrices together with tissue coordinates and images after initial processing with Space Ranger has already completed.
Run it here
The research agent runs nf-core/spatialvi with Nextflow on its own machine — up to 32 cores, 256 GiB of memory and 24 hours per run, which covers the test profile and real single-sample runs. It builds the samplesheet, checks it against the pipeline's schema and reads the results back. When a run is too big for one machine, it gives you the exact command for your own cluster instead.
Strengths and limits
Good at
- Accepts both raw sequence inputs via Space Ranger and datasets that have already undergone Space Ranger processing.
- Maintains modular, reproducible execution across environments using per-process Docker or Singularity containers.
- Routinely verified on full-scale datasets via continuous integration testing on AWS cloud infrastructure.
Watch out for
- Tailored specifically for 10x Genomics Visium data and does not support alternative spatial transcriptomics technologies.
- Workflow parameters cannot be passed via custom Nextflow configuration files and must be specified using the command line or parameter files.
Questions
Can I run nf-core/spatialvi without my own cluster?
The research agent runs nf-core/spatialvi with Nextflow on its own machine — up to 32 cores, 256 GiB of memory and 24 hours per run, which covers the test profile and real single-sample runs. It builds the samplesheet, checks it against the pipeline's schema and reads the results back. When a run is too big for one machine, it gives you the exact command for your own cluster instead.
What licence is nf-core/spatialvi under?
MIT, like every nf-core pipeline.
Can this pipeline process raw fastq files directly?
Yes. It can run 10x Genomics Space Ranger directly on raw inputs, or alternatively take inputs that have already been run through Space Ranger.
Which spatial transcriptomics assays are supported?
The pipeline is specifically designed for 10x Genomics Visium transcriptomics datasets.
How should parameters be provided when running the workflow?
Parameters must be provided using command-line arguments or via a Nextflow parameters file specified with -params-file. Custom configuration files cannot be used to pass pipeline parameters.
How to cite it
Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.
Written from nf-core/spatialvi's own README. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.