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
Project Samples
License
GNU General Public License version 3.0 (GPLv3)User Reviews
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Very useful and reliable package, it makes robust analysis but at the same time it´s easy to understand and especially to use. It has many functions so it covers 95% of the required steps to find sequence variants. I must say that honestly the tutorial is one of the few that is really well written and that that explains how to make the analysis step by step. You can go throughout it easily without previous knowledge and still be able to complete the whole SNPs identification and annotation. Additionally it has a very good balance between speed and reliable results.