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Supported Pipelines and Products

Supported Pipelines and Products

There are several ways to use the 10x Genomics Cloud Analysis platform for your data analysis: 1) web browser app, 2) command line (CLI) interface, and 3) prompt-based interface.

To help you decide the best method for your use case, review the pipeline analyses that are currently supported for each method in the tables below:

Single Cell Pipeline / Analysis10x Cloud Analysis web browser app10x Cloud Analysis Command Line (CLI) interface10x Cloud prompt-based interface
Cell Ranger count
(documentation)
Cell Ranger multi
(documentation for sample multiplexing, Flex, and V(D)J data)
Cell Ranger aggr
(documentation)
Cell Ranger vdj
(documentation)
Cell Ranger reanalyze
(documentation)
Data normalization with SCTransform
(documentation)
Batch correction with Harmony
(documentation)
Automated cell type annotation
(documentation)
Cell Ranger ARC count
(documentation)
Cell Ranger ARC aggr
(documentation )
Cell Ranger ARC reanalyze
(documentation)
Spatial Pipeline / Analysis10x Cloud Analysis web browser app10x Cloud Analysis Command Line (CLI) interface10x Cloud prompt-based interface
Space Ranger count
(documentation)

The supported pipeline version(s) and library types are listed by 10x Cloud Analysis method in the tables below.

Refer to the web browser app documentation for usage details.

Analysis PipelinesPipeline VersionLibrary Types
Space Ranger count
  • 4.0
  • 3.1, 3.0
  • Visium HD Spatial Gene Expression
  • Visium HD 3' Gene Expression
Cell Ranger count
  • 9.0
  • 8.0
  • 7.2, 7.1, 7.0
  • 6.1, 6.0
  • 5.0
  • 4.0
  • 3.1
  • Universal 3’ Gene Expression
  • Universal 5’ Gene Expression
  • Feature Barcode Libraries
    • Antibody Capture
    • Custom Library
Cell Ranger multi
  • 9.0
  • 8.0
  • 7.2, 7.1, 7.0
  • 6.1, 6.0
  • 5.0
  • 4.0
  • 3.1
  • Universal 3’ Gene Expression
  • Universal 5’ Gene Expression
  • Flex Gene Expression
  • Feature Barcode Libraries
    • Antibody Capture
    • CRISPR Guide Capture
    • Custom Library
    • Flex Antibody Capture
    • Flex CRISPR Guide Capture
  • Universal 5' V(D)J
  • Sample multiplexing
    • 3' CellPlex
    • On-chip multiplexing (OCM)
    • Hashing with Antibody Capture
Cell Ranger aggr
  • 9.0
  • 8.0
  • 7.2, 7.1, 7.0
  • 6.1, 6.0
  • 5.0
  • 4.0
  • 3.1
  • Universal 3’ Gene Expression
  • Universal 5’ Gene Expression
  • Flex Gene Expression
  • Feature Barcode Libraries
    • Antibody Capture
    • CRISPR Guide Capture
    • Custom Library
    • Flex Antibody Capture
    • Flex CRISPR Guide Capture
  • Universal 5' V(D)J
  • Sample multiplexing
    • 3' CellPlex
    • On-chip multiplexing (OCM)
    • Hashing with Antibody Capture
Cell Ranger vdj1
  • 9.0
  • 8.0
  • 7.2, 7.1, 7.0
  • 6.1, 6.0
  • 5.0
  • 4.0
  • 3.1
  • Universal 5' V(D)J
Cell Ranger reanalyze2
  • 9.0
  • 8.0
  • 7.2, 7.1, 7.0
  • 6.1, 6.0
  • 5.0
  • 4.0
  • 3.1
  • Universal 3' Gene Expression
  • Universal 5' Gene Expression
SCTransform/Harmony data integration workflow1.0
  • Universal 3' Gene Expression
  • Universal 5' Gene Expression
  • Flex Gene Expression
Cell Ranger annotate (Beta)0.2
  • Universal 3' Gene Expression
  • Universal 5' Gene Expression
  • Flex Gene Expression
Cell Ranger ARC count2.1, 2.0
  • Epi Multiome ATAC + Gene Expression
Cell Ranger ARC aggr2.1, 2.0
  • Epi Multiome ATAC + Gene Expression
Cell Ranger ARC reanalyze22.1, 2.0
  • Epi Multiome ATAC + Gene Expression

1 The 10x Cloud Platform does not support Cell Ranger vdj in de novo mode.

2Reanalysis of aggregated analyses (Cell Ranger) is not available in Cloud Analysis for the web browser.

Refer to the command-line interface documentation for installation and usage details.

Analysis PipelinesPipeline VersionLibrary Types
Space Ranger count4.0
  • Visium HD Spatial Gene Expression
  • Visium HD 3' Gene Expression
Cell Ranger count9.0
  • Universal 3’ Gene Expression
  • Universal 5’ Gene Expression
  • Feature Barcode Libraries
    • Antibody Capture
    • Custom Library
Cell Ranger multi9.0
  • Universal 3’ Gene Expression
  • Universal 5’ Gene Expression
  • Flex Gene Expression
  • Feature Barcode Libraries
    • Antibody Capture
    • CRISPR Guide Capture
    • Custom Library
    • Flex Antibody Capture
    • Flex CRISPR Guide Capture
  • Universal 5' V(D)J
  • Sample multiplexing
    • 3' CellPlex
    • On-chip multiplexing (OCM)
    • Hashing with Antibody Capture
Cell Ranger aggr9.0
  • Universal 3’ Gene Expression
  • Universal 5’ Gene Expression
  • Flex Gene Expression
  • Feature Barcode Libraries
    • Antibody Capture
    • CRISPR Guide Capture
    • Custom Library
    • Flex Antibody Capture
    • Flex CRISPR Guide Capture
  • Universal 5' V(D)J
  • Sample multiplexing
    • 3' CellPlex
    • On-chip multiplexing (OCM)
    • Hashing with Antibody Capture
Cell Ranger vdj19.0
  • Universal 5' V(D)J
Cell Ranger ARC count2.1
  • Epi Multiome ATAC + Gene Expression
Cell Ranger ARC aggr2.1
  • Epi Multiome ATAC + Gene Expression

1 The 10x Cloud Platform does not support Cell Ranger vdj in de novo mode.

Refer to the prompt-based interface documentation for installation and usage details.

Analysis PipelinesPipeline VersionLibrary Types
Cell Ranger count9.0
  • Universal 3’ Gene Expression
  • Universal 5’ Gene Expression
Cell Ranger multi9.0
  • Universal 3’ Gene Expression
  • Universal 5’ Gene Expression
  • Flex Gene Expression
  • Feature Barcode Libraries
    • Antibody Capture
    • CRISPR Guide Capture
    • Custom Library
    • Flex Antibody Capture
    • Flex CRISPR Guide Capture
  • Universal 5' V(D)J
  • Sample multiplexing
    • 3' CellPlex
    • On-chip multiplexing (OCM)
    • Hashing with Antibody Capture
Cell Ranger aggr9.0
  • Universal 3’ Gene Expression
  • Universal 5’ Gene Expression
  • Flex Gene Expression
  • Feature Barcode Libraries
    • Antibody Capture
    • CRISPR Guide Capture
    • Custom Library
    • Flex Antibody Capture
    • Flex CRISPR Guide Capture
  • Universal 5' V(D)J
  • Sample multiplexing
    • 3' CellPlex
    • On-chip multiplexing (OCM)
    • Hashing with Antibody Capture