Cell Ranger, printed on 08/05/2020
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, our PBMC_10k dataset, and version 3.0 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.