merAligner: A Fully Parallel Sequence Aligner

@article{Georganas2015merAlignerAF,
  title={merAligner: A Fully Parallel Sequence Aligner},
  author={Evangelos Georganas and Aydin Buluç and Jarrod Chapman and Leonid Oliker and Daniel Rokhsar and Katherine A. Yelick},
  journal={2015 IEEE International Parallel and Distributed Processing Symposium},
  year={2015},
  pages={561-570}
}
Aligning a set of query sequences to a set of target sequences is an important task in bioinformatics. In this work we present merAligner, a highly parallel sequence aligner that implements a seed -- and -- extend algorithm and employs parallelism in all of its components. MerAligner relies on a high performance distributed hash table (seed index) and uses one-sided communication capabilities of the Unified Parallel C to facilitate a fine-grained parallelism. We leverage communication… CONTINUE READING
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