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10x Genomics
Single Cell CNV

System Requirements

Cell Ranger DNA

Cell Ranger DNA pipelines are distributed for and run on 64-bit Linux systems. The runtime and storage requirements of Cell Ranger DNA scale linearly with the number of reads to be processed. In the recommended experiment (1000 cells at 750,000 read-pairs per cell) there will be 750 million read-pairs and the minimum system requirements are:

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

Software Dependencies

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

Resource Limits

LimitRecommendation
user open files 16k
system max files 10k per GB RAM available to Cell Ranger DNA
user processes 64 per core available to Cell Ranger DNA

Empirical Performance results

The performance data below was produced by running Cell Ranger DNA on a range of datasets and computers. Cell Ranger DNA runtime is almost entirely determined by the number of reads and is insensitive to the number of cells. The table below was created on hardware available from Amazon cloud services.

Performance results

Number of read-pairs Small system Medium system Large system
375 million 12h 6h 4h
1.2 billion 25h 13h 11h
7 billion Not recommended Not recommended 114h

System classification

CPU cores RAM (GB) CPU Generation Disk
Small system 16 128 Ivy Bridge HDD
Medium system 32 256 Broadwell HDD
Large system 48 384 Skylake SDD