Bioinformatics Software: Partek Flow

Partek Flow (now an Illumina software) is a web-based application for the analysis of bulk and single-cell sequencing data.  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 popular algorithms without writing codes or running command lines tools. The software features streamlined workflows for the analysis of all major NGS data types and excellent visualization functionalities for interactive data exploration. 

The Partek flow server is implemented on our 7-node custom condo HPC-NML in USC Advanced Research Computing (CARC). 

• For faculty and PhD-level research staff, CARC provides up to 10TB enterprise-level storage for free.  Additional storage can be requested for an annual fee. This storage will 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.

Chargeback fees apply for the use of Partek Flow through the USC license. 

To access Partek Flow:

1. Carefully review the Bioinformatics Software Chargeback Policy (pricing, billing, usage notes and tips) and the Partek Flow user policy.
2. Fill out and submit the Partek Flow Registration / USC NGS Data Analysis Service Request Form.
3. Partek Flow uses the PI’s CARC allocation for storing analysis data.  Instruction on setting up the PI’s CARC account will be sent to you and your PI once the above form is submitted.
4. Once the PI’s CARC account is ready, we will email you within two business days:
   • Your Partek Flow account information
   • Partek Flow server access instruction
   • Data upload instruction
5. Once your data are ready, we will set up an initial meeting to walk you through the analysis set up in Partek Flow
   • Before our initial meeting
     • Partek Flow Basic Components
     • Bulk RNA-Seq Analysis
     • scRNA-Seq Data Analysis – Basic
     • scRNA-Seq Data Analysis – Advanced
6. In most cases, we will set up a follow-up meeting to go over with you the initial analysis results.

Help @ Illumina

• Partek Flow online documentation
  • Quick Start Guide
  • Live Training Event Recordings
  • Tutorials
• Contact Illumina support: techsupport@illumina.com 

Help @ USC Libraries Bioinformatics Service

• Email us: nmlbio@usc.edu
• Onsite training: check on-site training schedules.