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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 HPC-NML Custom Condo and NML Bioinformatics Workstations.

Main Features

Tools in Partek Flow

Partek Flow Servers @ USC

HPC-Flow: cluster implementation on our 9-node custom condo HPC-NML in USC Advanced Research Computing (CARC). Most users will be set up on HPC-Flow.

  • Shorter analysis time powered by parallel processing.
  • For faculty and PhD-level research staff, CARC provides up to 10TB enterprise-level storage for free.  This storage can be used by Partek Flow directly for data analysis. 
  • CARC project account/storage application and configuration instructions will be sent to you upon NGS data analysis request form submission.  See Access Partek Flow section below. 

 

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

  • Large memory workstation computers are capable of handling specific memory-intensive tasks.

 

Important Note:

The USC Libraries Bioinformatics Service DO NOT provide storage services.  Unless using your own CARC project account storage, as soon as the project concludes, you must archive and export your analysis (a one-click function in Partek Flow) to your own storage, such as a lab computer, a USB drive, etc.  The archived project is in zip format and contains all input and result files.  It can be easily restored in Partek Flow for future analysis. 

Access Partek Flow

USC has licensed Partek Flow for the free use of USC faculty, students and staff. 

To access Partek Flow:

  1. Carefully read the Partek Flow user policy
  2. Fill out and submit the USC NGS Data Analysis Service Request Form
  3. Upon receiving the request, we will email you within two business days:
    • Your Partek Flow account information
    • Partek Flow server access instruction
    • Data upload instruction
  4. Once your data are ready, we will set up an initial meeting to walk you through the analysis set up in Partek Flow
  5. In most cases, we will set up a follow-up meeting to go over with you the initial analysis results

Need Help?

Help @ Partek Inc.

Help @ USC Libraries Bioinformatics Service