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HPC for Bioinformatics

Cineca is building a user-friendly bioinformatics environment supporting data analysis for several organisms on Pico architecture. The bioinformatics software, available both through the web interface and a standard unix module environment, will be continuously updated and complemented with all the public data (genomes, annotations, software indexes) necessary to carry on an efficient, reliable and consistent analysis of the user data.
Access to these resources for Italian researchers can be obtained through the ELIXIR-IIB HPC @CINECA service provided by ELIXIR-IIB, the Italian node of the european Infrastructure for Bioinformatics. 
 
Cineca provides the following NGS pipelines implemented with a user-friendly web interface: 
1. Deep targeted exome sequencing; 
2. RNA sequencing (trascriptome analysis); 
3. Whole exome sequencing; 
4. Identification of DNA protein interactions by ChiP-seq; 
5. RNA editing prediction by RNA-seq.  
 
These automatic pipelines may integrate other codes and/or steps after discussion of a motivated request. Here you can find further details.
 
All the bioinformatic software involved in the pipelines (e.g. bwa, bowtie, tophat, star for short read aligners or picard, samtools, bedtools as efficient utilities) are also available on Pico as unix module applications. In addition modules not included in the web pipelines (e.g. velvet, Ray for de-novo assembling) are also available for the users.  
 
The user can load environment variables pointing to the public data necessary to his/her analysis by selecting a specific module in the biodata category: 
 
------------ /cineca/prod/modulefiles/base/biodata ------------ 
D_melanogaster/dm3 Homo_Sapiens/hg19 Mus_musculus/mm9 
Homo_Sapiens/hg18 Mus_musculus/mm10 R_norvegicus/rn4
...  
 
If your research requires other open access bioinformatics software or you work on organisms not already installed on Pico, please notify us. We will schedule their installation.