DamageProfiler: fast damage pattern calculation for ancient DNA

Judith Neukamm; Alexander Peltzer; Kay Nieselt

doi:10.1093/bioinformatics/btab190

DamageProfiler: fast damage pattern calculation for ancient DNA

Bioinformatics. 2021 Oct 25;37(20):3652-3653. doi: 10.1093/bioinformatics/btab190.

Authors

Judith Neukamm^{1

2

3}, Alexander Peltzer^{2

4}, Kay Nieselt²

Affiliations

¹ Institute of Evolutionary Medicine, University of Zurich, 8057 Zurich, Switzerland.
² Institute for Bioinformatics and Medical Informatics, University of Tübingen, 72076 Tübingen, Germany.
³ Institute for Archaeological Sciences, University of Tübingen, 72070 Tübingen, Germany.
⁴ Max Planck Institute for the Science of Human History, 07745 Jena, Germany.

PMID: 33890614
DOI: 10.1093/bioinformatics/btab190

Abstract

Motivation: In ancient DNA research, the authentication of ancient samples based on specific features remains a crucial step in data analysis. Because of this central importance, researchers lacking deeper programming knowledge should be able to run a basic damage authentication analysis. Such software should be user-friendly and easy to integrate into an analysis pipeline.

Results: DamageProfiler is a Java-based, stand-alone software to determine damage patterns in ancient DNA. The results are provided in various file formats and plots for further processing. DamageProfiler has an intuitive graphical as well as command line interface that allows the tool to be easily embedded into an analysis pipeline.

Availability and implementation: All of the source code is freely available on GitHub (https://github.com/Integrative-Transcriptomics/DamageProfiler).

Supplementary information: Supplementary data are available at Bioinformatics online.