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To set up and run Cell Ranger on Linux, please follow the steps below, or skip download and installation and get started with 10x Cloud Analysis.
- Check system requirements
- Download Cell Ranger
- Download References (Optional)
- Download Probe Sets (Optional)
- Install Cell Ranger
- 10x Genomics Cloud Analysis (Optional)
Cell Ranger 9.0.1 (Feb 6, 2025)
- Chromium Single Cell 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.
- View Cell Ranger source code on GitHub
tar.gz compression
Download for Linux 64-bit (tar.gz)File size: 807 MBmd5sum: 2efec98bff01f7a59edaf43724fae13fcurlwgetcurl -o cellranger-9.0.1.tar.gz "https://cf.10xgenomics.com/releases/cell-exp/cellranger-9.0.1.tar.gz?Expires=1743533240&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA&Signature=bDzbCCq85R9rSA9m7fr07yV9zw-cvvynU63WaF8WSXV9qAvJLfWWd3D9Xm1FKEUNHM~cs3S9mkvBjbSECMeTGkdTqTJhoa2U3L3Fil4j18XZT4YQKTTjTb2gFlQfSHUruL4N8GwLbxI3BsDsIOWYzgiE7qPjqyxvZuqu2S119RaLfyB0FY9crkw3dq5V4TBBA7xU05AaSpYMzVnwJ5TxxYJdqcBjSsJJ-S2XvzkKmsZo5~cNZ4tuaCG5tN2u~KEb7c44qPRMTu3X7k70Poi5GITiRCZSjzioEFOVA3DlM1hXXlb85Q2wIqTw0efIHT9MBPtqFSjkwXD40GQNZnT3yA__"tar.xz compression
Download for Linux 64-bit (tar.xz)File size: 538 MBmd5sum: 540fe4256c8d12d7f701303983ed3d48curlwgetcurl -o cellranger-9.0.1.tar.xz "https://cf.10xgenomics.com/releases/cell-exp/cellranger-9.0.1.tar.xz?Expires=1743533240&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA&Signature=TZA02uDUaLbhGB2jEXpIAuao6K8vWNZ~gBY1BleOVQ3I4tYfWNoxddtggVVVtXGSL5dECIJUbGJpeszXA1GiZ3hm-FC8LzmuV--iqr4PjMb3QiUu-99Ee4shahPSGRgcng10P1oAHBFxuc7AEWgNYTlvO8xpCkEwHDQk7Gluw7EDxdqCU-A32PsqnmF5oVTJfljr48unWZBdSHT3jt4jjqJhw17rh0z2AqUs9OpRyR4toJ6chSaFewh2nriKiK6cCMuLU7TtHrBHd8ZL3Khe6QOU-AWv80hBiJ02eAvfjaKr9JwibUmZEpxVy20h2sBHBdTBTQH4Dez48LlG94d~RQ__"
Download is unavailable on mobile devices.
Cell Ranger 9.0.1 highlights
- Supports the analysis of GEM-X Universal 3' and 5' Gene Expression Multiplex libraries
- Cell Ranger now enables automated cell type annotations
- Starting with v9.0, anonymized telemetry data is collected and sent to 10x Genomics
- v9.0.1 includes minor updates and bug fixes
References
New versions of the human and mouse reference transcriptomes based on the Ensembl v110 annotations are now available for download. Details are available in the reference release notes.
Human reference (GRCh38) - 2024-A
- Human reference (GRCh38) dataset required for Cell Ranger.
Download Human ReferenceFile size: 11 GBmd5sum: a7b5b7ceefe10e435719edc1a8b8b2facurlwgetcurl -O "https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCh38-2024-A.tar.gz"Mouse reference (GRCm39) - 2024-A
- Mouse reference (GRCm39) dataset required for Cell Ranger.
Download Mouse ReferenceFile size: 9.7 GBmd5sum: 37c51137ccaeabd4d151f80dc86ce0b3curlwgetcurl -O "https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCm39-2024-A.tar.gz"Rat reference (mRatBN7.2) - 2024-A
- Rat reference (mRatBN7.2) dataset required for Cell Ranger.
Download Rat ReferenceFile size: 9.5 GBmd5sum: 34d4af0874a45dfa03436efe4eaec2fecurlwgetcurl -O "https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mRatBN7-2-2024-A.tar.gz"Human (GRCh38) and mouse (GRCm39) reference - 2024-A
- Human (GRCh38) and mouse (GRCm39) reference dataset for Cell Ranger.
Download ReferenceFile size: 11 GBmd5sum: b2d628e6c6813e1396989a9a9ca2ef23curlwgetcurl -O "https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCh38_and_GRCm39-2024-A.tar.gz"
Download is unavailable on mobile devices.
Human V(D)J reference (GRCh38)
- Human reference (GRCh38/Ensembl/10x) dataset required for Cell Ranger V(D)J.
Download Human ReferenceFile size: 3.3 MBmd5sum: 65b5b033723b07fc1bb5375e5645761ccurlwgetcurl -O "https://cf.10xgenomics.com/supp/cell-vdj/refdata-cellranger-vdj-GRCh38-alts-ensembl-7.1.0.tar.gz"Mouse V(D)J reference (GRCm38)
- Mouse reference (GRCm38/Ensembl/10x) dataset required for Cell Ranger V(D)J.
Download Mouse ReferenceFile size: 3.5 MBmd5sum: c6f41db8f67aa83b04d64ba1ae96e681curlwgetcurl -O "https://cf.10xgenomics.com/supp/cell-vdj/refdata-cellranger-vdj-GRCm38-alts-ensembl-7.0.0.tar.gz"
Download is unavailable on mobile devices.
Probe Sets v1.1
The Flex 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 setsProbe Barcode Sequence
Human Transcriptome
- Probe Set CSV
Input for cellranger multi pipeline
- Probe Set Metadata TSV
- Probe Set BED
- Possible Off-Target Probes CSV
Mouse Transcriptome
- Probe Set CSV
Input for cellranger multi pipeline
- Probe Set Metadata TSV
- Probe Set BED
- Possible Off-Target Probes CSV
Other downloads
Sample Index Set Sequences
- Chromium Single Cell 3' v2 CSV
- Chromium Single Cell 3' v2 JSON
- Chromium Single Cell 3' v1 CSV
- Chromium Single Cell 3' v1 JSON
- Gemcode Single Cell 3' CSV
- Gemcode Single Cell 3' JSON
- Chromium Single Cell 5' CSV
- Chromium Single Cell 5' JSON
- Chromium Single Cell 5' with Feature Barcodes CSV
- Chromium Single Cell 5' with Feature Barcodes JSON
Telemetry
Compute Platforms
View options for compute platforms
System requirements
View the minimum requirements to run Cell Ranger pipelines
Installation
View instructions on how to install Cell Ranger