Correcting errors in shotgun sequences

Sequencing errors in combination with repeated regions cause major problems in shotgun sequencing, mainly due to the failure of assembly programs to distinguish single base differences between repeat copies from erroneous base calls. In this paper, a new strategy designed to correct errors in shotgun sequence data using defined nucleotide positions, DNPs, is presented. The method distinguishes single base differences from sequencing errors by analyzing multiple alignments consisting of a read and all its overlaps with other reads. The construction of multiple alignments is performed using a novel pattern matching algorithm, which takes advantage of the symmetry between indices that can be computed for similar words of the same length. This allows for rapid construction of multiple alignments, with no previous pair-wise matching of sequence reads required. Results from a C++ implementation of this method show that up to 99% of sequencing errors can be corrected, while up to 87% of the single base differences remain and up to 80% of the corrected reads contain at most one error. The results also show that the method outperforms the error correction method used in the EULER assembler. The prototype software, MisEd, is freely available from the authors for academic use.