Supported Pipelines and Products


Analysis Pipeline Status Version Library Types
Cell Ranger count Supported v6.1
v6.0
v5.0
v4.0
v3.1
  • Single Cell 3' Gene Expression
  • HTStandardLT
  • Single Cell 5' Gene Expression
  • HTStandard
  • Targeted Single Cell 3' Gene Expression
  • HTStandard
  • Targeted Single Cell 5' Gene Expression
  • HTStandard
  • Feature Barcode Libraries
    • Antibody Capture
    • CRISPR Guide Capture
    • Custom Library
Cell Ranger multi Supported v6.1
v6.0
  • Single Cell 3' Gene Expression
  • HTStandardLT
  • Single Cell 5' Gene Expression
  • HTStandard
  • Targeted Single Cell 3' Gene Expression
  • HTStandard
  • Targeted Single Cell 5' Gene Expression
  • HTStandard
  • Feature Barcode Libraries
    • Antibody Capture
    • CRISPR Guide Capture
    • Custom Library
  • Single Cell V(D)J
  • Multiplexing Capture (3' only)
Cell Ranger aggr Supported v6.1
v6.0
v5.0
v4.0
v3.1
  • Single Cell 3' Gene Expression
  • HTStandardLT
  • Single Cell 5' Gene Expression HTStandard
  • Targeted Single Cell 3' Gene Expression
  • HTStandard
  • Targeted Single Cell 5' Gene Expression
  • HTStandard
  • Feature Barcode Libraries
    • Antibody Capture
    • CRISPR Guide Capture
    • Custom Library
  • Single Cell V(D)J
  • Multiplexing Capture (3' only)
Cell Ranger V(D)J Supported v6.1
v6.0
v5.0
v4.0
v3.1
  • Single Cell V(D)J
Cell Ranger reanalyze1 Supported v6.1
v6.0
v5.0
v4.0
v3.1
  • Single Cell 3' Gene Expression
  • HTStandardLT
  • Single Cell 5' Gene Expression HTStandard
  • Targeted Single Cell 3' Gene Expression
  • HTStandard
  • Targeted Single Cell 5' Gene Expression
  • HTStandard
Cell Ranger ARC count Supported v2.0.1
v2.0.0
  • Single Cell Multiome ATAC + Gene Expression
Cell Ranger ARC aggr Supported v2.0.1
v2.0.0
  • Single Cell Multiome ATAC + Gene Expression
Cell Ranger ARC reanalyze1 Supported v2.0.1
v2.0.0
  • Single Cell Multiome ATAC + Gene Expression

Legend

HT High Throughput Learn more
Standard Standard Kit
LT Low Throughput Learn more

1 At this time, reanalysis of aggregated count runs is not available in Cloud Analysis.

More on Supported Pipelines