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10x Genomics Single Cell Flow Cell Calculator

10x Genomics Visum Spatial Transcriptome Calculator


This calculator will help determine the correct flow cell selection to achieve necessary read depth on a Visium Spatial project.

The sequencing parameters and number of cycles required for the different single cell applications can be found on the core's 10x Genomic page.



Number of Array Tiles (4 tiles per slide)        

Percentage of Area Covered                             (enter as value between 0 and 1; ex. 60% = 0.6)

Spots per tile                     =   5,000

Targeted Reads Per spot   =   50,000 read pairs

Total Reads Required      

(No. Tiles) * (percentage of tile covered) * (5,000 spots/tile) * (Targeted Reads Per spot)

                    Flow Cell Use Ratio*
NovaSeq X Lane (2-digit precision)     
Estimated sequencing cost                      $

*A ratio of 1.0 indicates a 100% usage of the flow cell. This would be the best match of flow cell to output need for the sequencing.

Assumptions used in calculations:

  • NovaSeq X flow cell (lane) = 1.25 billion paired reads