title: Improving ancient DNA genome assembly.
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 novoassembly has to be used. However, because of inherent problems with ancient DNA, itsde novoassembly 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 two different ancient samples and compared the results to currentde novoassembly approaches. We are able to improve the assembly with respect to the length of the contigs and can resolve more repetitive regions.
authors.affiliation: Center for Bioinformatics (ZBIT), Integrative Transcriptomics, Eberhard-Karls-Universität Tübingen , Tübingen , Germany.
authors.forename: Alexander
authors.initials: A
authors.lastname: Seitz
authors.affiliation: Center for Bioinformatics (ZBIT), Integrative Transcriptomics, Eberhard-Karls-Universität Tübingen , Tübingen , Germany.
authors.forename: Kay
authors.initials: K
authors.lastname: Nieselt
keywords: Ancient DNA; De novo assembly; Genome reconstruction