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HPC for Next Generation Sequencing

High-Performance Bioinformatics Services for Next Generation Sequencing data analysis in Public Health and Research

Next-generation DNA sequencing (NGS) has incredibly accelerated biological and biomedical research, by allowing the comprehensive analysis of genomes, transcriptomes and interactomes. Managing the huge amount of data from new sequencing platforms requires non trivial skills, strong computational power and storage capacity which are generally not available in most research labs. Our consortium has been recognized as big data center and HPC analysis for the Italian epigenomic flag project Epigen and is member of ELIXIR-IIB the Italian node of the european Infrastructure for Bioinformatics. 

The CINECA centralized bioinformatics core facility provides shared resources for the computational and IT requirements. 

E-mail Contacts: hpc-bioinformatics or superc

Whole Genome/Exome and Taget Exome Analysis Pipeline

CoVaCS is an automated, highly accurate workflow for genotyping, variant calling and annotation for Next Generation Sequencing data. By integrating state of the art tools and algorithms in a swift and effective manner and providing a extensive collection of reference genomes, CoVaCS offer the possibilty to perform elaborate and comprehensive genotyping of NGS data even to users with little or no bioinformatic background.

CoVaCS is currently hosted at CINECA and benefits all the advantages of HPC computing.

In its current form CoVaCS offers pre-configured workflows for the analyses of WGS, WES and targeted resequencing data.

All the workflows are very simple to use and require little configuration by the users:

WGS workflow: to be used if your data is complete shotgun sequencing of any of the reference genomes in CoVaCS, all you need to do is tell CoVaCS which reference genome is to be used.

WES workflow: if you performed exome sequencing on any of man,mouse or cow, CoVaCS is capable to handle all the major commercial exome kits (Illumina, Agilent or Nimblegen) for you, all you have to do is select the right kit (and reference genome!) from the dropdown menu.

Targeted resequencing workflow: this workflow is intended for targeted resequencing experiments, but it comes handy also in the case where you can't find your exome kit enlisted among the kits included in CoVaCS. To inform the system of the target regions, you will have to supply CoVaCS the coordinates in the format of a bed file. Please be sure to that your file matches the same version of the genome assembly you are intend to use before starting any analyses.

CoVaCS is designed to offer a simple stremalined, GUI driven workflow for the analysis of NGS resequencing data, as such the user is given little or no means to modify the behaviour of our workflows. If you are an advanced user and feel the need of a more elaborate and customizable pipeline for genotyping, you can use the command line based version of CoVaCS.

Disclaimer: This pipeline is currently unavailable for human genomic data due to EU GDPR privacy regulation.



RNA-Seq (Transcriptome) analysis is now avaliable for transcriptome structural analysis and quantification. The transcriptome analysis allows the identification of known or novel expressed transcript variants, and their quantification.
RNA-Seq, unlike microarrays, does not require prior knowledge of the genome and therefore offers several advantages. Our facility, RAP, can study the transcriptome profiling of each sample, performing differential gene expression analysis, cassette exons detection, identification of chimeric transcripts and polyA sites detection.


Data Repository for the Network for Italian Genomes

The NIG fosters genetics and genomics research in broad sense with special reference to Italian population. Defining an Italian Reference Genome will be useful for the identification of:

  • genes responsible for genetic diseases and susceptibility genes for complex diseases in both basic and translational researches,
  • genetic variants responsible for interindividual differences in drug response in the Italian population, and useful for population and forensic purposes
  • new target for diagnosis and treatment of genetic diseases

NIG-db only publishes aggregated variant frequencies from a pool of data provided by the submitters.