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

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.