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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

  • Accept all major types of NGS data in all common file formats:
    RNA-seq, DNA-seq, ChIP-seq, miRNA-seq, smallRNA-seq, Methylation-seq
  • Support all major NGS platforms:
    Illumina, Applied Biosystems, Roche 454, Helicos, Ion Torrent
  • Direct upload of sequence read files from all major sequencers
  • Web-based user-friendly interface enables easy access, data management, collaboration, workflow history, and task scheduling
  • Pre- and post-alignment QC/QA, subsampling and trimming.
  • Multiple aligners with recommended defaults yet fully customizable
    TopHat, TopHat2, STAR, BWA, Bowtie, Bowtie2, TMAP, SHRiMP2, GSNAP, Issac2
  • Embedded RNA-seq workflow uses a sophisticated Gene Specific Analysis method to determine the best model for each gene's expression pattern.
  • Variant detection using SamTools, FreeBayes, LoFreq, Strelka, and GATK.
  • Fusion genes detection
  • Chromosome view

Access @ USC

USC has licensed Partek Flow for the free use of USC faculty, students and staff.  We have two types of Partek Flow servers:

  1. On our dedicated 10-nodes custom condo in USC High-Performance Computing network.
    Following an initial setup, users with USC HPC account can access our HPC Flow server using a web-browser anywhere in the world. 
  2. On our workstation computers
    Following an initial setup, users can access the Flow servers via a web-browser on USC network.  When off the campus, users will need a USC VPN connection before accessing the server.  The workstation-based Flow servers are physically available at the following locations:
  • Norris Medical Library (RM203A), the Health Sciences Campus.
  • Wilson Dental Library,  the University Park Campus.

To request your free access of Partek Flow:

  1. Carefully read the Partek Flow user policy
  2. Fill out and submit the  USC NGS Data Analysis Service Request Form
  3. First-time users are required to meet with the USC Libraries Bioinformatics Service team for initial training and analysis set up.‚Äč

Need Help?

Get started

Help @ Partek Inc.

  • The user-friendly Partek support team can initiate web-conference and show you the procedures interactively on your computer screen
  • Contact Partek support

Help @ USC Libraries Bioinformatics Service