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.
Download and run online this app named NGSEP with OnWorks for free.
Follow these instructions in order to run this app:
- 1. Downloaded this application in your PC.
- 2. Enter in our file manager https://www.onworks.net/myfiles.php?username=XXXXX with the username that you want.
- 3. Upload this application in such filemanager.
- 4. Start the OnWorks Linux online or Windows online emulator or MACOS online emulator from this website.
- 5. From the OnWorks Linux OS you have just started, goto our file manager https://www.onworks.net/myfiles.php?username=XXXXX with the username that you want.
- 6. Download the application, install it and run it.
SCREENSHOTS
Ad
NGSEP
DESCRIPTION
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
Features
- 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
Audience
Healthcare Industry, Science/Research, Other Audience, Agriculture
User interface
Java SWT, Console/Terminal, Eclipse
Programming Language
Java
Categories
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.
