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Quality-score guided error correction for short-read sequencing data using CUDA

: Shi, Haixiang; Schmidt, Bertil; Liu, Weiguo; Müller-Wittig, Wolfgang K.

Postprint (PDF; )

Procedia computer science. Online journal 1 (2010), Nr.1, S.1129-1138
ISSN: 1877-0509
International Conference in Computational Science (ICCS) <10, 2010, Amsterdam>
Zeitschriftenaufsatz, Konferenzbeitrag, Elektronische Publikation
Fraunhofer IGD ()
Compute Unified Device Architecture (CUDA); Bioinformatics; DNA sequencing

Recently introduced new sequencing technologies can produce massive amounts of short-read data. Detection and correction of sequencing errors in this data is an important but time-consuming pre-processing step for de-novo genome assembly. In this paper, we demonstrate how the quality-score value associated with each base-call can be integrated in a CUDA-based parallel error correction algorithm. We show that quality-score guided error correction can improve the assembly accuracy of several datasets from the NCBI SRA (Short-Read Archive) in terms of N50-values as well as runtime. We further propose a number of improvements of to our previously published CUDA-EC algorithm to improve its runtime by a factor of up to 1.88.