ngsep

We have hosted the application ngsep in order to run this application in our online workstations with Wine or directly.

Quick description about ngsep:

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 (https: //sourceforge.net/p/ngsep/wiki/Home/).

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

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.

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