Genomics Workbench

The RIGSC has a dedicated computer, a MacPro with 2 x 2.66 GHz 6-core Intel Xeon processors, set up with Genomics Workbench 8.0.2 software by CLCbio for analyzing, comparing, and visualizing Next Generation Sequencing (NGS) data.  CLC Genomics Workbench is a comprehensive analysis package, which can analyze and visualize data from all major NGS platforms, such as SOLiD, 454, Illumina and Ion Torrent and it supports key NGS features within genomics, transcriptomics and epigenomics.

Some of the features of Genomics Workbench include:

Genomics

  • Read mapping of Sanger, 454, Illumina and SOLiD sequencing data
  • De novo assembly of genomes of any size (only limited by RAM available)
  • Color space mapping
  • Advanced visualization, scrolling, and zooming tools
  • Resequencing tools (variant detection and downstream analysis)
  • Support for multiplexing with DNA barcoding

Transcriptomics

  • RNA-seq including support for paired data and transcript- level expression
  • Small RNA analysis
  • Expression profiling by tags
  • EST library construction
  • Advanced visualization, scrolling, and zooming tools
  • Gene expression analysis

Epigenomics

  • ChIP-seq analysis
  • Peak finding and peak refinement
  • Case/control analysis

Classical sequence analysis tools

  • Primer design
  • Molecular cloning
  • BLAST
  • Alignments
  • Phylogenetic trees
  • Advanced RNA structure prediction and editing
  • Integrated 3D molecule analysis
  • Secondary protein structure predictions

The CLC Genomics Workbench is licensed for a single user.  A beginner’s Genomics Workbench Guide with instructions in how to use the software is available.  Please contact the RIGSC manager at 401-874-5919 or pwj419@uri.edu for more information on using the Workbench.

The RIGSC acknowledges the support of the Rhode Island Agricultural Experiment Station (RIAES), the College of Environment and Life Sciences and the Division of Research and Economic Development for the software and equipment.