NGSEP (Next Generation Sequencing Experience Platform)

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Download NGSEPplugin_3.0.2.201701221824.jar
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NGSEP now is much more than the plugin so we decided to rebrand it as Next Generation Sequencing Experience Platform. NGSEP is an integrated framework for analysis of high throughput sequencing reads with several deployment alternatives for different kinds of users. The main functionality of NGSEP is the variants detector, which allows to make simultaneous discovery of SNVs, indels, and CNVs. We also provide a user interface for bowtie2, alignments sorting, merging of variants from different samples, functional annotation, filtering, format conversion, and several additional features.

Note: Since we offer different distribution alternatives for different kinds of users, the quick download (green) button may not lead you to the version of the product that you need. Please visit our web page to choose the distribution of NGSEP that better suits your needs.

NGSEP Web Site


  • SNPs, CNVs and Structural Variants detection
  • Functional Annotation
  • VCF manipulation: merge, filter, compare, format conversion
  • SAM/BAM and VCF statistics calculation and plotting
  • Reads Deconvolution
  • Genotype Imputation
  • Graphical interface for Bowtie2 mapping
  • Web Deployment through integration with Galaxy
  • A graphical interface within the Cyverse collaborative platform


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Additional Project Details

Intended Audience

Healthcare Industry, Science/Research, Other Audience, Agriculture

User Interface

Java SWT, Console/Terminal, Eclipse

Programming Language




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