BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btu368 Sequence analysis Advance Access publication June 11, 2014 Blue: correcting sequencing errors using consensus and context

Motivation: Bioinformatics tools, such as assemblers and aligners, are expected to produce more accurate results when given better quality sequence data as their starting point. This expectation has led to the development of stand-alone tools whose sole purpose is to detect and remove sequencing errors. A good error-correcting tool would be a transparent component in a bioinformatics pipeline, simply taking sequence data in any of the standard formats and producing a higher quality version of the same data containing far fewer errors. It should not only be able to correct all of the types of errors found in real sequence data (substitutions, insertions, deletions and uncalled bases), but it has to be both fast enough and scalable enough to be usable on the large datasets being produced by current sequencing technologies, and work on data derived from both haploid and diploid organisms