DACCOR - Detection, charACterization, and reconstruction of Repetitive regions in bacterial genomes
- Published
- Accepted
- Subject Areas
- Bioinformatics, Computational Biology
- Keywords
- NGS, repeat resolution
- Copyright
- © 2017 Seitz et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2017. DACCOR - Detection, charACterization, and reconstruction of Repetitive regions in bacterial genomes. PeerJ Preprints 5:e3480v1 https://doi.org/10.7287/peerj.preprints.3480v1
Abstract
The reconstruction of genomes using mapping based approaches with short reads experiences difficulties when resolving repetitive regions. These repetitive regions in genomes result in low mapping qualities of the respective reads, which in turn lead to many unresolved bases of the genotypers. Currently, the reconstruction of these regions is often based on modified references in which the repetitive regions are masked. However, for many references such masked genomes are not available or are based on repetitive regions of other genomes. Our idea is to identify repetitive regions in the reference genome de novo. These regions can then be used to reconstruct them separately using short read sequencing data. Afterwards the reconstructed repetitive sequence can be inserted into the reconstructed genome. We present the program DACCOR, which performs these steps automatically. Our results show an increased base pair resolution of the repetitive regions in the reconstruction of Treponema pallidum samples, resulting in fewer unresolved bases.
Author Comment
The contents of this paper were presented at the GCB2017 as a poster.