Bioinformatics Software: Partek Flow

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.

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.

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
   • Before our initial meeting
     • Partek Flow Basic Components
     • Bulk RNA-Seq Analysis
     • scRNA-Seq Data Analysis – Basic
     • scRNA-Seq Data Analysis – Advanced
5. In most cases, we will set up a follow-up meeting to go over with you the initial analysis results

Help @ Partek Inc.

• Partek Flow user documentation
• The user-friendly Partek support team can initiate web-conference and show you the procedures interactively on your computer screen
• Contact Partek support
  • by phone: 314.884.6177 (9am - 5pm CST)
  • by email: support@partek.com

Help @ USC Libraries Bioinformatics Service

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