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HPC for Bioinformatics

Cineca is building a user-friendly bioinformatics environment supporting data analysis regarding several model organisms on Galileo architecture. The bioinformatics software, tools and annotation are available through a unix module environment, built in a modular fashion therefore continuously updated and complemented with the public data (e.g. reference genomes, genomic variant annotations, genomic indexes and more) necessary to carry on an efficient, reliable and consistent data analysis.
The user can have a look at the available resources and load  the environment variables pointing to the necessary stuff for his/her analysis by digiting the command “modmap -p bioinf” after having logged in Galileo.

Bioinformatics researchers can access to computing, storage and specialist support resources through the ISCRA calls or the ELIXIR-ITA HPC@CINECA calls provided by ELIXIR-IIB, the Italian node of the European intergovernmental organisation that is made up of life scientists, computer scientists and support staff for Bioinformatics. If you whish to know more about these calls and have an overview about some stories of success, please refer to this paper.
Besides the command line module environment, CINECA provides the following NGS automated pipelines implemented with a user-friendly web interface which can be used also by researchers without bioinformatics skills: 
  1.  RNA sequencing analysis (gene and transcript expression, differential expression, alternative splicing, polyA signals and gene fusion transcript detection). DOI
  2. Target Exome and Whole exome/genome sequencing. DOI.

Morover, thanks  to a a PRACE project with funded from the EU’s Horizon 2020 research and innovation programmel, it was recently developed an HPC-aware (multicore and multinode) Software for a large scale analysis of RNA editing detection events by RNA-seq samples.  
If your research requires further open access bioinformatics resources or if you work on model organisms not yet available on Galileo, please notify us by e-mail and we will schedule their installation.