NGSEP - Download

Free download NGSEP Linux app to run online in Ubuntu online, Fedora online or Debian online

This is the Linux app named NGSEP whose latest release can be downloaded as It can be run online in the free hosting provider OnWorks for workstations.

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NGSEP is an integrated framework for analysis of DNA high throughput sequencing data. The main use of NGSEP is the construction and downstream analysis of large datasets of genomic variation. NGSEP performs accurate detection and genotyping of Single Nucleotide Variants (SNVs), small and large indels, short tandem repeats (STRs), inversions, and Copy Number Variants (CNVs). NGSEP also provides modules for functional annotation, filtering, format conversion, comparison, clustering, imputation, introgression analysis and different kinds of statistics. A complete list of functionalities is available in our wiki (

NEWS: We just made available the first version of our de-novo genomes assembler. Further details are available in the wiki.


  • De-novo genomes assembly
  • Alignment of raw reads to a reference genome
  • SNPs, CNVs and Structural Variants detection
  • VCF manipulation: functional annotation, merge, filter, compare, format conversion, imputation
  • Reads Demultiplexing
  • Alignment of annotated genome assemblies
  • Statistics and filtering on transcriptome annptations in GFF3 format


Healthcare Industry, Science/Research, Other Audience, Agriculture

User interface

Java SWT, Console/Terminal, Eclipse

Programming Language


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