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Cell Ranger


10x Genomics
Single Cell Gene Expression

System Requirements


Cell Ranger pipelines run on Linux systems that meet these minimum requirements:

Note: Version 6.1 is the last version that will support CentOS/RedHat 6 or Ubuntu 12.04. Future versions will require CentOS/RedHat 7 or newer, or Ubuntu 14.04 or newer.

See the 10x Genomics OS Support page for further information.

In order to run in cluster mode, the cluster needs to meet these additional minimum requirements:


In order to run cellranger mkfastq, the following software needs to be installed:

Resource Limits

Limit Recommendation
user open files 16k
system max files 10k per GB RAM available to Cell Ranger
user processes 64 per core available to Cell Ranger

How Memory Affects Runtime

The following plots are based on time trials using Amazon EC2 instances and version 6.1 of Cell Ranger. Observed performance will be impacted by other factors besides memory, including library type (whole transcriptome vs. targeted), read depth, number of cells, number of cores/threads, and I/O. The plots below are meant to convey how increasing memory beyond the minimum and recommended levels may impact runtime for large datasets run with cellranger multi, cellranger count, and cellranger aggr, but may not be representative of your dataset.

Shown below is cellranger multi walltime as a function of memory for a 60k cell CellPlex dataset:


Here is cellranger count walltime as a function of memory for a 20k PBMC high throughput dataset:

20k count

Here is cellranger aggr walltime as a function of available memory for a 250k cell dataset. In general, performance can be improved by allocating more than the minimum 64GB of memory to the pipeline.