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Genome Assembly Using an Asynchronous Distributed Actor-Based Approach

DescriptionWe use genome assembly as a representative case to showcase the use of the ‘actor model’, a novel programming system for high-performance data-intensive workloads. The actor version of the 𝑘-mer counting kernel shows on average 1.6× speedup over similar MPI implementation. We provide a novel parallel algorithm that leverages the actor model to traverse de Bruijn graphs in a non-blocking, one-directional manner. Our findings highlight the potential of the actor model for writing simple and efficient parallel programs for data-heavy workloads.

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