@article{bowtie-bwa:ff:multicore:biomed:14,
  keywords = {fastflow,bioinformatics},
  url = {http://downloads.hindawi.com/journals/bmri/2014/539410.pdf},
  title = {Sequence alignment tools: one parallel pattern to rule them all?},
  author = {Claudia Misale and Giulio Ferrero and Massimo Torquati and Marco
            Aldinucci},
  abstract = {In this paper we advocate high-level programming methodology for
              Next Generation Sequencers (NGS) alignment tools for both
              productivity and absolute performance. We analyse the problem of
              parallel alignment and review the parallelisation strategies of
              the most popular alignment tools, which can all be abstracted to a
              single parallel paradigm. We compare these tools against their
              porting onto the FastFlow pattern-based programming framework,
              which provides programmers with high-level parallel patterns. By
              using a high-level approach, programmers are liberated from all
              complex aspects of parallel programming, such as synchronisation
              protocols and task scheduling, gaining more possibility for
              seamless performance tuning. In this work we show some use case in
              which, by using a high-level approach for parallelising NGS tools,
              it is possible to obtain comparable or even better absolute
              performance for all used datasets. },
  year = {2014},
  journal = {BioMed Research International},
}

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