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Motivation: Next generation methods of DNA sequencing produce relatively highrate of reading errors, which interfere with de novo genome assembly of newlysequenced organisms and particularly affect the quality of SNP detectionimportant for diagnostics of many hereditary diseases. There exists a number ofprograms developed for correcting errors in NGS reads. Such programs utilizevarious approaches and are optimized for different specific tasks, but all ofthem are far from being able to correct all errors, especially in sequencingreads that crossing by repeats and DNA from di/polyploid eukaryotic genomes.Results: This paper describes a novel method of error correction based onclustering of alignments of similar reads. This method is implemented inReadsClean program, which is designed for cleaning Illumina HiSeq sequencingreads. We compared ReadsClean to other reads cleaning programs recognized to bethe best by several publications. Our sequence assembly tests using actual andsimulated sequencing reads show superior results achieved by ReadsClean.Availability and implementation: ReadsClean is implemented as a standalone Ccode. It is incorporated in an error correction pipeline and is freelyavailable to academic users at Softberry web server www.softberry.com.

ReadsClean: a new approach to error correction of sequencing reads based on alignments clustering