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PAGANtec: Openmp parallel error correction for next-generation sequencing data

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Abstract

Next-generation sequencing techniques reduced the cost of sequencing a genome rapidly, but came with a relatively high error rate. Therefore, error correction of this data is a necessary task before assembly can take place. Since the input data is huge and error correction is compute intensive, parallelizing this work on a modern shared-memory system can help to keep the runtime feasible. In this work we present PAGANtec, a tool for error correction of next-generation sequencing data, based on the novel PAGAN graph structure. PAGANtec was parallelized with OpenMP and a performance analysis and tuning was done. The analysis led to the awareness, that OpenMP tasks are a more suitable paradigm for this work than traditional work-sharing.

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Joppich, M., Schmidl, D., Bolger, A. M., Kuhlen, T., & Usadel, B. (2015). PAGANtec: Openmp parallel error correction for next-generation sequencing data. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 9342, pp. 3–17). Springer Verlag. https://doi.org/10.1007/978-3-319-24595-9_1

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