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The new protocol for sequencing the messenger RNA
in a cell, named RNA-seq produce millions of short sequence
fragments. Next Generation Sequencing technology allows more
accurate analysis but increase needs in term of computational
resources. This paper describes the optimization of a RNA-seq
analysis pipeline devoted to splicing variants detection, aimed
at reducing computation time and providing a multi-user/multisample
environment. This work brings two main contributions.
First, we optimized a well-known algorithm called TopHat by
parallelizing some sequential mapping steps. Second, we designed
and implemented a hybrid virtual GRID infrastructure allowing
to efficiently execute multiple instances of TopHat running on
different samples or on behalf of different users, thus optimizing
the overall execution time and enabling a flexible multi-user
environment
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