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Cell Ranger


10x Genomics
Single Cell Gene Expression

System Requirements

Table of Contents


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

Note: Cell Ranger v6.1 was the last version that supported CentOS/RedHat 6 or Ubuntu 12.04.

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

Software dependencies

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 7.0 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 wall time as a function of memory for a 60k cell 3' Cell Multiplexing dataset:


Here is cellranger multi wall time as a function of memory for a 16-plex Fixed RNA Profiling dataset run with BAM file generation on and off:

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

20k count

Here is cellranger aggr wall time 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.