Download Space Ranger - Official 10x Genomics Support

10x Genomics Support/Space Ranger/

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To set up and run Space Ranger, please follow the following steps:

Space Ranger 2.1.0 (May 16, 2023)

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 14.04.
Runs on Linux systems that meets the minimum compute requirements.

tar.gz compression
Download for Linux 64-bit (tar.gz)
File size: 707 MB
md5sum: ee94c453c44770b2b69d6be46b948e3e
- curl
- wget
```
curl -o spaceranger-2.1.0.tar.gz "https://cf.10xgenomics.com/releases/spatial-exp/spaceranger-2.1.0.tar.gz?Expires=1695953592&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA&Signature=NyTq-5p77u0CaSaI1OrQj75mJi7kJhEBNsO~wWsrgzv~3Pt4iG4rHRYaBcTbQK2eh47kTzIwAkCjtmSWGnGRS4GYuDbEzBK8oC-cLWaLpOrkU6OjRiRqc1a~l6ix26vWkyvphw2ZLSchS9mZGrrJ14~dLdv5dpUh1kOqVSbIoQrDFmTB5lzY5oR3qVT9gc5mFBgg5eTrTtamAynsIOfhfBHT7FmXFz74bg~Nh6hN0aH1eZy0ohiw37RPl1-pxNjxyMRBZZvD2B1bCSu0ehSlireso4JOjl6JmlA-onvE6Wiw6r9n3CaJeR3T~SpZ~a~io~zNs7oTbF9U8dCUEYa4EA__"
```

tar.xz compression

Download for Linux 64-bit (tar.xz)

File size: 465 MB

md5sum: a0d90129a81c41cbdd728e23a4d25161

curl
wget


curl -o spaceranger-2.1.0.tar.xz "https://cf.10xgenomics.com/releases/spatial-exp/spaceranger-2.1.0.tar.xz?Expires=1695953592&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA&Signature=YTrfYBDcgA8CAHvPe8YLKMHWB~w~fbbpkNbe6GdkHW0PEyRYLP4wVVz6jPy4Phn14RZvLjxh-G8wwasxWQK-EiW6gWZUERjdehO7QQRdjV~EaS4lCLLhqt5chZALA5wOmTLp4AH07Z1q3A1WCyLcnkh~cPlbB0uR4SN6fF6z7-GAj6Fk7NpETqVFPBsfqVwR802ugF8Onr4cmbrxL2xJG9WYl-cPTL9~siPrmot0J6QUpFAlMw2Zyf48zs-eNemfNvp92jHoKA7Gx5sai41uO2eCJJS19Mv2wv9iUuLktEWLQZUkzvfCOwm8EB6~-vjibgI89c0BDxIdgDZsQ33tYw__"

Download is unavailable on mobile devices.

Space Ranger 2.1.0 highlights

New feature: Gene + Protein Expression on Visium CytAssist.
New feature: Reference-free spot deconvolution.
Added support for bigtiff (btf, tf2, and tf8) image file extensions.

Release notes

Previous versions

References

We observe sensitivity gains in the analysis with the 2020-A reference compared to the previous cellranger/spaceranger reference. These are mainly due to an updated transcriptome annotation (Ensembl 93 → 98) and improved filtering of readthrough gene annotations. A number of genes (notably IGLC1) are uncounted or undercounted without this filtering step. Below are gains in sensitivity that we observed.

1-3% relative increase in Median UMI Counts per spot
1-2% relative increase in Median Genes per spot
4-7% relative increase in Total Genes Detected
1-3% increase in Reads Mapped Confidently to Transcriptome
0.5% decrease in Reads Mapped Confidently to Intergenic Regions

Details about the specific steps used to correct these annotations can be found in the reference build scripts.

Human reference (GRCh38) dataset required for Space Ranger.
- Human reference (GRCh38) dataset required for Space Ranger.
Download Human Reference
File size: 110.178 MB
md5sum: 26151804338ae4d4b44151232bd64b50
- 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) dataset required for Space Ranger.
Download Mouse Reference
File size: 110.178 MB
md5sum: 24ee09ad620a9eb2753763fa068edf1f
- 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

The Visium for FFPE and the Visium CytAssist Spatial Gene and Protein Expression for FFPE assays use probes targeting protein coding genes in the human or mouse transcriptomes. Each probe consists of a pair of oligonucleotides hybridized to the targeted transcript and are subsequently ligated.

View more details about probe sets

Other downloads

Sample Index Set Sequences

System requirements

View the minimum requirements to run Space Ranger pipelines

Installation

Space Ranger Installation

View instructions on how to install Space Ranger