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Bioinformatics Software: Partek Flow

Overview

Partek Flow is a web-based application for the data analysis of next generation sequencing including RNA, small RNA, and DNA sequencing.  With an easy-to-use graphical interface and the ability to build custom analysis pipelines or download existing ones, Partek Flow enables bench top researchers to carry out routine NGS data analysis using dozens of popular algorithms without writing codes or running command lines tools. The software features streamlined workflows for RNA-seq, DNA-seq, ChIP-seq, and Single cell sequencing data analysis that uses popular algorithms for NGS raw data QA/QC, alignment, visualization, as well as RNA quantification and variant detection.  

Partek Flow has been implemented on both HPCC-NML Custom Condo and NML Bioinformatics Workstations.

Main Features

Tools in Partek Flow

Partek Flow Servers @ USC

HPC-Flow: cluster implementation on our 14-node custom condo in USC High-Performance Computing (USC HPC). For most users, we will set you up on HPC-Flow.

  • Free enterprise-level storage for up to 5TB per user provided by USC HPC
  • Shorter analysis time powered by parallel processing
  • Remote transfer files using FileZilla or other FTP utilities
  • Use of USC HPC requires active USC account (NetID)
  • The initial setup of an USC HPC account may take up to 2 weeks 

 

Stand-alone Partek Flow servers: single server implementation on our workstation computers

  • No initial setup required.
  • Large memory workstation computers are capable of handling specific memory-intensive tasks. 
  • In this case, we ask that you bring your raw data files on an external hard drive to one of offices:
    • NML 203A, Health Sciences Campus
    • CEM 202, University Park Campus

Access Partek Flow

USC has licensed Partek Flow for the free use of USC faculty, students and staff.  To request your access:

Step 1. Apply for an USC HPC account following this instruction.  If any of the following situations apply to you, proceed directly to step 2.  

  • You don't have an active USC email account (@usc.edu).  That includes CHLA employees who only have @chla.usc.edu emails.
  • You will leave USC within a year. 
  • You won't have any more NGS data in the foreseeable future. 
  • The NGS data is in urgent need (less than 2 weeks) 

 

Step 2. Submit a NGS analysis request

Your first project in Partek Flow

Need Help?

Help @ Partek Inc.

 

Help @ USC Libraries Bioinformatics Service