Download Space Ranger - Official 10x Genomics Support

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To set up and run Space Ranger, follow these steps:

Space Ranger 3.1.1 (Sep 9, 2024)

Visium Spatial Software Suite
Self-contained, relocatable tar file. Does not require centralized installation.
Contains binaries pre-compiled for CentOS/RedHat 7.0 and Ubuntu 16.04.
Runs on Linux systems that meets the minimum compute requirements.

tar.gz compression
Download for Linux 64-bit (tar.gz)
File size: 827 MB
md5sum: c0b9a274d7d3692e28f086818eb55e62
curl
wget
```
curl -o spaceranger-3.1.1.tar.gz "https://cf.10xgenomics.com/releases/spatial-exp/spaceranger-3.1.1.tar.gz?Expires=1732259235&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA&Signature=TYSnXoexJ810yjEHgBubWxHhseq~E1kiH-k99cViLDuHqBrvqM4DFpaE1sg7Br5KcfhnI2lAlTuvdcquA3nkOp5s5srwX5SRPkkk6685ZiH3MEmh2ZtIHb8K52JuTfcobrwqTR-ggPnHJ7Y57YE2iEy6fTYoqBhqyDq-bAIevD5LKJkMl4fQe4ySlVxdIf6-PfkiLFinXCR-X30YFR-6bDe7~XUjWIiesNhc8sw6nW~GZHqsPHDtEDsczxNLhS2PjZb-BafOvLoBR3Wse-YpkTR~jhvT9gvpHdRdAyGwlqhY6J6BCdqoPOJUoWVMa0EtOI0XsKRcXTKoXvqY9cBgMg__"
```

tar.xz compression

Download for Linux 64-bit (tar.xz)

File size: 527 MB

md5sum: 4adde78374877cee92d056b903a77759

curl

wget


curl -o spaceranger-3.1.1.tar.xz "https://cf.10xgenomics.com/releases/spatial-exp/spaceranger-3.1.1.tar.xz?Expires=1732259235&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA&Signature=JEP7l8VK4AFe4EQ7veAhY-asG5ASjNlD0-HY7KZizUUrBEVjeyd1DZWzL-IrUzUvAZsovUiJn-O5myEi7WMfpvoap9mIv3orlnvCmTdxmY4s7ZFsgod6wyqBwdS9hGj3RBJkMl8gz~KpOsv-itXjDuiipGM4Ja8sI87HDRAglYThWrxbPjQHpYf9ppGITPN91cuEmM42gZfWP0HxP9m5NuA6IGWFPOs97TU9fW70RHBAhEa7yYghPSfkm7PJJEk509REgWkCAdqiXjJG-I1DRFl06yPlM30qd7rjWjSoV6zPnGwsZ3inzCCz6UxceK83SlvcKsy-nUlnH1y-~itL~w__"

Download is unavailable on mobile devices.

Space Ranger v3.1.1 highlights

In Space Ranger v3.1.1, the pipeline has been overhauled to significantly improve the CytAssist to microscope image registration process.

Previous versions

Release notes

References

References are required to run the spaceranger count pipeline. 10x Genomics offers pre-built human and mouse references for download. You can alternatively create a custom reference.

Human reference (GRCh38)
- Human reference (GRCh38)
Download Human Reference
File size: 11 GB
md5sum: dfd654de39bff23917471e7fcc7a00cd
curl
wget
```
curl -O "https://cf.10xgenomics.com/supp/spatial-exp/refdata-gex-GRCh38-2020-A.tar.gz"
```
mm10 Reference - 2020-A (June 23, 2020)
- Mouse reference (mm10)
Download Mouse Reference
File size: 9.7 GB
md5sum: 886eeddde8731ffb58552d0bb81f533d
curl
wget
```
curl -O "https://cf.10xgenomics.com/supp/spatial-exp/refdata-gex-mm10-2020-A.tar.gz"
```

Download is unavailable on mobile devices.

Probe Sets

Visium probe-based assays target genes in the human or mouse transcriptomes. For these assays, it is required to specify the relevant probe set to the spaceranger count pipeline. Probe sets come bundled with the Space Ranger package and are also available for download here for convenience.

View more details about probe sets

Slide File Download

If Space Ranger is to be run in an environment without access to the Internet, the pipeline will require a Visium slide layout file using the --slidefile option. Enter the slide serial number below to download the corresponding slide layout file.

Other downloads

Sample Index Set Sequences

Feature Reference CSV Files

Human Immune Cell Profiling Panel

System requirements

View the minimum requirements to run Space Ranger pipelines

Installation

Space Ranger Installation

View instructions on how to install Space Ranger