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Because of the large size of single cell RNA-Seq data sets and the computationally-intensive tools used in single cell analysis, we have amended our system requirements and recommendations for installations with the Single Cell toolkit. 

Up to 100,000 cells per analysis

Required

• Linux:

 Ubuntu

• Ubuntu® 12.04, Redhat®

61

• 6.10, CentOS® 6.10, or newer

• CPU: 64-bit 2 GHz quad-core processor

• Memory: 64 GB of

RAM 

• RAM

• Local scratch space

: None

• ¹: 1 TB with cached or native speeds of 2GB/s or higher

• Storage:

 1

• 1 TB available for data

Recommended

• Linux:

 Ubuntu

• Ubuntu®

 12

• 16.04, Redhat®

 61

• 7.6, CentOS®

 6

• 7.6, or newer

• CPU: 64-bit 2 GHz quad-core processor

• Memory: 128 GB of

RAM 

• RAM

• Local scratch space

: 500 GB with cached

• ¹: 2 TB with cached or native speeds of 2GB/s or higher

• Storage:

 1

• 1 TB available for data

More than 100,000 cells per analysis

Required

• Linux:

 Ubuntu

• Ubuntu®

 12

• 16.04, Redhat®

 61

• 7.6, CentOS®

 6

• 7.6, or newer

• CPU: 64-bit 2 GHz quad-core processor

• Memory: 256 GB of

RAM 

• RAM

• Local scratch space¹:

 1

• 2 TB

with cached

• with cached or native speeds of 2GB/s or higher

• Storage:

 1

• 4 TB available for data

Recommended

• Linux:

 Ubuntu

• Ubuntu®

 12

• 16.04, Redhat®

 61

• 7.6, CentOS®

 6

• 7.6, or newer

• CPU: 64-bit 2 GHz quad-core processor

• Memory: 512 GB of

RAM 

• RAM

• Local scratch space¹:

1

• 10 TB

with cached

• with cached or native speeds of 2GB/s or higher

• Storage:

 1

• 10 TB available for data

For fastest performance:

• Newer generation CPU cores with avx2 or avx-512 are recommended.

• Performance scales proportionality to the number of CPU cores available.

• Hyper thread cores (threads) scales performance for most operations other than principal component analysis.

Optimization tips for Cluster installations¹ Contact Partek support for recommended setup of local scratch storage