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Because of the large size and specialized tools used for analyzing 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 of Partek Flow with the Single Cell toolkit. 

Up to 100,000 cells per analysis

Required

• Linux:

 Ubuntu

• Ubuntu^®

12

• 18.04, Redhat^®

61

• 8, CentOS^®

6

• 8, 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

•   > 2 TB available for data and > 100 GB on the root partition

Recommended

• Linux:

 Ubuntu

• Ubuntu^®

 12

• 18.04, Redhat^®

 61

• 8, CentOS^®

 6

• 8, 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

•   > 2 TB available for data and > 100 GB on the root partition

More than 100,000 cells per analysis

Required

• Linux:

 Ubuntu

• Ubuntu^®

 12

•  18.04, Redhat^®

 61

•  8, CentOS^®

 6

•  8, 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

•  18.04, Redhat^®

 61

•  8, CentOS^®

 6

•  8, 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 installations

 ¹ Contact Partek support for recommended setup of local scratch storage

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