NGS & Bioinformatics
The Next Generation Sequencing (NGS) and Bioinformatics platforms are the core of the EPIGEN project. The Institute of Applied Genomics in Udine runs an NGS service dedicated exclusively to EPIGEN partners. The data generated are managed and stored in a repository created by CASPUR/CINECA.
Several EPIGEN teams develop softwares and pipelines for NGS data analysis, here below is a list of bioinformatic tools which have been recently developed and published.
Click here to access a complete overview of the resource usage among EPIGEN users. You need to be registered with an EPIGEN account to display the overview.
ExpEdit is a tool for the analysis of RNA editing using RNA-Seq data
ASPicDB allows the prediction of alternative spliced transcripts.
RAP is a web tool that performs a quite complete and customizable RNA-Seq pipeline and provides an easy and intuitive access through a web interface to intermediate and final results.
WEP is a web-tool that allows to run a complete whole-exome sequencing pipeline and provides easy access through interface to intermediate and final results.
Check it out at http://epigen.hpc.cineca.it/wep/
FIDEA was designed to facilitate the functional interpretation of differential expression analyses.
Cscan allows to identify common regulators of a set of genes using ChIP-Seq datasets.
Pscan allows to search for transcription factor binding sites in promoters of co-regulated or co-expressed genes.
MoD Tools contains a collection of softwares for the search of motifs on DNA and RNA.
ERNE is a highly performing and sensitive aligner for short (NGS-like) reads.