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Partek Flow: Overview


Partek Flow is a web-based application that uses popular algorithms for NGS raw data QA/QC, alignment, visualization, as well as RNA quantification and variant detection.  In addition to an embedded sophisticated RNA-seq workflow, the aligned reads can be transferred seamlessly to Partek Genomics Suite for advanced statistical and functional analysis.

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,BWA, Bowtie, Bowtie2, TMAP, SHRiMP2
  • Embedded RNA-seq workflow uses a sophisticated Gene Specific Analysis method to determine the best model for each gene's expression pattern.
  • Variant detection (SNP and indel)
  • Fusion genes detection
  • Chromosome view

Access @ USC

To use Partek Flow, complete and submit the Partek Flow Access Request Form.  Your needs will be evaluated and you will be sent follow-up instructions within two business days.  Please note that first-time  Partek Flow users are required to meet with the Norris Medical Library Bioinformatics Service for initial training and analysis set up.


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Help @ Partek Inc.

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

Help @ NML Bioinformatics