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10x Genomics
Chromium Single Cell Immune Profiling

System Requirements

Table of Contents


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.

The pipelines also run on clusters that meet these additional minimum requirements:

Software dependencies

Most software dependencies come bundled in the Cell Ranger package. However, cellranger mkfastq also requires:

Resource limits

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 for the cellranger vdj pipeline

This graph is based on time trials using Amazon EC2 instances and version 6.1.2 of Cell Ranger. Observed performance will be impacted by other factors besides memory, including read depth, number of cells, number of cores/threads, and I/O. The graph is meant to convey how increasing memory beyond the minimum and recommended levels may impact runtime for large datasets run with cellranger vdj. Similar graphs for cellranger multi, cellranger count, and cellranger aggr are provided on the 3' Single Cell Gene Expression's System Requirements page, but may not be representative of your dataset.

Walltime as a function of memory for a 10k PBMC V(D)J T cell dataset, read depth ~6,500 reads/cell: