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

• 8-core Intel or AMD processor (64 cores recommended), which support the AVX+ instruction set, introduced in 2011 on both Intel and AMD CPUs. AVX2 will be required in the future, introduced in 2013 on Intel CPUs and in 2015 on AMD CPUs.
• 64 GB RAM (128 GB recommended).
• 1.5 TB free disk space.
• 64-bit CentOS/RedHat 7.0 or Ubuntu 14.04. See the 10x Genomics OS Support page for additional details.

Larger datasets require additional resources. The following table indicates the requirements to keep runtimes less than 3 days for representative small, medium, and large datasets:

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

• Shared filesystem (e.g. NFS)
• Slurm batch scheduling system

Running Cell Ranger in cluster mode is recommended for large datasets.

Cell Ranger v9.0 introduced support for generating automated cell type annotations (beta pipeline). To use this optional feature, you will need a 10x Genomics Cloud Analysis account and a stable internet connection, as your data will be transmitted to the cloud for processing.

Most software dependencies come bundled in the Cell Ranger package. However, cellranger mkfastq (deprecated) also requires Illumina bcl2fastq v2.20 or later.

• Cell Ranger runs locally by default (or when specified as --jobmode=local), using 90% of available memory and all of the available cores. To restrict resource usage, please use the --localmem and --localcores options (see cellranger vdj --help).

• Many Linux systems have default user limits (ulimits) for maximum open files and maximum user processes as low as 1024 or 4096. Because Cell Ranger spawns multiple processes per core, jobs that use a large number of cores can exceed these limits. We recommend higher limits:

The following table is based on time trials using Amazon EC2 instances and Cell Ranger v10.0. Empirical performance will be impacted by numerous factors, including processors, RAM, hard disks, library type, read depth, number of cells, number of cores/threads, and I/O. The data are meant to convey how increasing dataset size may impact Cell Ranger's performance, but may not be representative of your dataset.