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Cytognomix Shannon Pipeline

The splicing mutation pipeline plugin finds and interprets genomic variants that alter mRNA splicing in human exome, targeted sequencing, or complete genome data.

Cytognomix genome-scale human splicing mutation analysis.

Shannon pipeline from Cytognomix was initially created to address the vexing problem of assessing the many variants of unknown significance that are detected in cancer genetic testing. The Shannon human splicing mutation plug-in uses a proven approach to predict mRNA splicing abnormalities based on single nucleotide variant data from human sequencing. The Cytognomix plugin can be deployed on CLC Genomics workbench either as a standalone application or to CLC Genomics server using the Genomics Workbench client.


The Cytognomix Shannon plugin identifies splicing mutations with industry-leading sensitivity and specificity. It is based on a legacy of peer-reviewed literature confirming validated mutation predictions using our patented information theory based technology. Changes in information content in splice sites correspond to actual differences in binding affinity. Input can either be CLC bio SNP objects, in standard VCF, or an indexed simple SNP format. Results are based on sensible default parameters, are sortable and intuitive, and exportable to spreadsheets or genome browsers.

Summary of changes in version 2.0

  • Runs on Windows Vista, 7, or 8 (64 bit)
  • Is approximately 12 times faster than version 1.0
  • Handles insertions and deletions (beta)
  • Performs gene set (or pathway overrepresentation analysis) on mutated gene lists
  • Simplifies post-run analysis with preset filters for functionally significant variants
  • Updated to include RefSeq gene annotations


The Shannon pipeline has been used to reanalyze the Breast Cancer Information Core identifying many splicing mutations, most of which were previously unrecognized (Mucaki et al. 2011) .

Splicing mutations in 3 complete cancer cell line genomes were identified with the Shannon pipeline and were validated by transcriptome analysis (Shirley et al. 2013) .

Learn more about the Shannon pipeline plugin in this video from Cytognomix:

Versioning and Requirements

The Cytognomix Shannon human mRNA splicing plugin runs in standalone mode on either the CLC Genomics Workbench V6.5, or with both the Workbench Client and CLC Genomics Server V6.5 (as a standalone server or grid-enabled). Released for the following 64 bit operating systems: Windows (Vista, 7, 8), Linux, and MacOSX. This plugin requires at least 4Gb of RAM. To facilitate variant annotation and information analysis, a dependency plugin must be installed for the appropriate genome build (GRCh37/hg19 or NCBI36/hg18).


Further Reading


The plugin is easily installed from within the Workbench:

  1. Click Plugins in the Toolbar
  2. Click the tab Download Plugins
  3. Select the plugin you wish to install
  4. Click the Download and Install button

Download from

Alternatively, you can download the plugin.

Workbench Download Server Download