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

Hardware

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

• 8-core Intel or AMD processor (16 cores recommended)
• 64GB RAM (128GB recommended)
• 1TB free disk space
• 64-bit CentOS/RedHat 6.0 or Ubuntu 12.04

| | The minimum requirement of 64GB RAM will allow cellranger aggr to aggregate up to 250k cells, more memory will be required beyond that. |

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:

• 8-core Intel or AMD processor per node
• 6GB RAM per core
• Shared filesystem (e.g. NFS)
• SGE or LSF batch scheduling system

Software

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

• Illumina® bcl2fastq: bcl2fastq must be version 2.20 or higher.

Resource Limits

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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 CPU and Memory Affect Runtime

| | The following plots are based on time trials using Amazon EC2 instances, one of our public datasets, and version 4.0 of Cell Ranger. These plots will not be updated with every subsequent release of Cell Ranger, unless pipeline performance changes significantly. |

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Memory

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