Improving ancient DNA genome assembly
- Published
- Accepted
- Subject Areas
- Bioinformatics, Paleontology, Computational Science
- Keywords
- ancient DNA, de novo assembly, genome reconstruction
- Copyright
- © 2016 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
- 2016. Improving ancient DNA genome assembly. PeerJ Preprints 4:e2383v1 https://doi.org/10.7287/peerj.preprints.2383v1
Abstract
Most reconstruction methods for genomes of ancient origin that are used today require a closely related reference. In order to identify genomic rearrangements or the deletion of whole genes, de novo assembly has to be used. However, because of inherent problems with ancient DNA, its de novo assembly is highly complicated. In order to tackle the diversity in the length of the input reads, we propose a two-layer approach, where multiple assemblies are generated in the first layer, which are then combined in the second layer. We used this two-layer assembly to generate assemblies for an ancient sample and compared the results to current de novo assembly approaches. We are able to improve the assembly with respect to the length of the contigs and can resolve more repetitive regions.
Author Comment
This is an article which has been accepted for the "GCB 2016 Conference".