Improvements of robustness and scalability of the Echo corrector of sequencing errors

Department of Experimental Biology, Faculty of Science, Masaryk University


The original implementation of Echo, despite of being based on very robust algorithm, was designed to deal with small sized sequencing data. We reimplemented the algorithm to deal with large data and to leverage parallelism—speedup up to 40x and 10x reduction of memory footprint was achieved. The new implementation allows handling large data sets which was not feasible before. The work carries on with defining methods of thorough evaluation of the implementation correctness which is not trivial for a randomized algorithm.

Results

  • Ištvánek J., Jaroš M, Křenek A, and Řepková J. Genome assembly and annotation for red clover (Trifolium pratense; Fabaceae). American Journal of Botany, St Louis: Botanical Soc Amer Inc, 2014, 101, 2, pp. 327-337.

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