Cell Ranger, printed on 04/18/2021
Cell Ranger pipelines run on Linux systems that meet these minimum requirements:
|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:
In order to run cellranger mkfastq, the following software needs to be installed:
|user open files||16k|
|system max files||10k per GB RAM available to Cell Ranger|
|user processes||64 per core available to Cell Ranger|
|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.|
Here is cellranger count walltime as a function of available memory. In general, you can improve performance by allocating more than the minimum 64GB of memory to the pipeline. If your system has ≫128GB of memory, you may want to run with --localmem=128 since there is notable diminishing return beyond 128GB.
Here's cellranger count walltime as a function of threads. If your system has ≫32 logical cores, you may want to run with --localcores=32 since there is diminishing return beyond 32 threads.