NGSEP (Next Generation Sequencing Eclipse Plugin)

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NGSEP (Next Generation Sequencing Eclipse Plugin), an integrated framework for analysis of high throughput sequencing reads. The main functionality of NGSEP is the variants detector, which allows to make simultaneous discovery of SNVs, indels, and CNVs.

NGSEP also provides a user interface for bowtie2 to perform mapping to the reference genome and other utilities such as alignments sorting, merging of variants from different samples, and functional annotation of variants. NGSEP is based on Eclipse which is one of the leading development environments for Java.

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 the web page to choose the distribution of NGSEP that better suits your data analysis environment.

NGSEP Web Site


  • SNPs, CNVs and Structural Variants detection
  • Functional Annotation
  • VCF manipulation: merge, filter, compare, format conversion
  • SAM/BAM manipulation: sorting, clipping
  • SAM/BAM and VCF statistics calculation and plotting
  • Reads Deconvolution
  • Genotype Imputation
  • Graphical interface for Bowtie2 mapping


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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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