Illumina error correction near highly repetitive DNA regions improves de novo genome assembly.

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 pa

SUBMITTER: Heydari M 

PROVIDER: S-EPMC6545690 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature