DamageProfiler: fast damage pattern calculation for ancient DNA

Judith Neukamm, Alexander Peltzer, Kay Nieselt

2021Bioinformatics147 citationsDOI

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.

Topics & Concepts

Computer sciencePipeline (software)JavaSource codeSoftwareGraphical user interfaceAuthentication (law)Code (set theory)Application programming interfaceSource lines of codeScripting languageProgramming languageData miningComputer securitySet (abstract data type)Forensic and Genetic ResearchEnvironmental DNA in Biodiversity StudiesPaleopathology and ancient diseases