The advent of Next Generation Sequencers (NGS)has driven the necessity to design new and more sophisticated tools in order to cope with the huge amount of data produced by these novel technologies. String alignment against a genome reference is the first and most important phase in every(re)-sequencing project. Recently, distributed tools able to align large amounts of sequences using clusters or clouds of computers, have been put forward. The aim of this work is to propose a new tool named mrNA (the MPI version of the original rNA program) able to align NGS data using a cluster of computers. mrNA was designed to tackle the main computational bottleneck of all classical parallel implementation of aligners: references longer than 4 Gbp. mrNA, together with rNA, are open source programs downloadable at http://iga-rna.sourceforge.net/. © 2011 IEEE.