Abstract:
BACKGROUND : Several standalone error correction tools have been proposed to correct sequencing errors in Illumina
data in order to facilitate de novo genome assembly. However, in a recent survey, we showed that state-of-the-art
assemblers often did not benefit from this pre-correction step. We found that many error correction tools introduce
new errors in reads that overlap highly repetitive DNA regions such as low-complexity patterns or short
homopolymers, ultimately leading to a more fragmented assembly.
RESULTS : We propose BrownieCorrector, an error correction tool for Illumina sequencing data that focuses on the
correction of only those reads that overlap short DNA patterns that are highly repetitive in the genome.
BrownieCorrector extracts all reads that contain such a pattern and clusters them into different groups using a
community detection algorithm that takes into account both the sequence similarity between overlapping reads and
their respective paired-end reads. Each cluster holds reads that originate from the same genomic region and hence
each cluster can be corrected individually, thus providing a consistent correction for all reads within that cluster.
CONCLUSIONS : BrownieCorrector is benchmarked using six real Illumina datasets for different eukaryotic genomes. The
prior use of BrownieCorrector improves assembly results over the use of uncorrected reads in all cases. In comparison
with other error correction tools, BrownieCorrector leads to the best assembly results in most cases even though less
than 2% of the reads within a dataset are corrected. Additionally, we investigate the impact of error correction on
hybrid assembly where the corrected Illumina reads are supplemented with PacBio data. Our results confirm that
BrownieCorrector improves the quality of hybrid genome assembly as well. BrownieCorrector is written in standard
C++11 and released under GPL license. BrownieCorrector relies on multithreading to take advantage of
multi-core/multi-CPU systems. The source code is available at https://github.com/biointec/browniecorrector.
