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NGSEP download for Linux

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 NGSEPwindows_4.3.2.zip. 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 short and long DNA high throughput sequencing reads. The current version provides functionalities for both de-novo and reference guided analysis of sequencing data, including genome assembly, read mapping, variants detection and genotyping and de-novo analysis of data generated from reduced representation protocols. NGSEP also provides modules for analysis of genomic variation databases (VCF files), including functional annotation, filtering, format conversion, comparison, clustering, imputation, introgression analysis and different kinds of statistics. Since version 4, we provide functionalities for management of genomes and transcriptomes, including genome alignment and annotation of transposable elements. A complete list of functionalities is available in our wiki (https://sourceforge.net/p/ngsep/wiki/Home/).

BEFORE DOWNLOADING: The green button directs to the jar for command line usage. See the wiki for the GUI and other options


  • 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



Bio-Informatics, Information Analysis

This is an application that can also be fetched from https://sourceforge.net/projects/ngsep/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.

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