STSM – Stefano Beretta


Stefano Beretta


Università degli Studi di Milano – Bicocca, Milan, Italy

Corresponding WG


Grant research topic

the Usage of HPC Techniques for Developing Models of Genetic Information

Hosting Institution

University of Stirling, Stirling, United Kingdom


2016-02-29 to 2016-03-13

Summary of the scientific report

At the beginning of the visiting period, a departmental seminar titled “Approaches for Haplotype Assembly viaMinimum Error Correction” illustrating the problem of reconstructing the haplotypes of anindividual, starting from a set of sequencing data, was done. Its aim wasto discussthe state of the art of algorithmic approaches for solving thehaplotype assembly, modeledas Minimum Error Correction problem, and two FPT proposals to solve it: WhatsHap and HapCol. Possible ways to improve and/or combine the two approaches presented in the talk have been discussed bringing together my expertise onHapCol and the one of Dr. Andrea Braccialiwho workedon an HPC implementation of WhatsHap. Draft ideas that could lead to improvements on the above mentioned problems have been outlined during the two-week STSM.

Personal notes

It was a great experience and everything was perfectly organized by Dr. Andrea Bracciali. I’ve been provided with an office at the department of Computing Science and Mathematics, and also an access at the facilities of the University of Stirling was granted.