DamageProfiler: Fast damage pattern calculation for ancient DNA

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. Here, we present DamageProfiler, 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.

[1]  Adrian W. Briggs,et al.  Preparation of next-generation sequencing libraries from damaged DNA. , 2012, Methods in molecular biology.

[2]  Alexander Peltzer,et al.  Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager , 2020, bioRxiv.

[3]  C. Warinner,et al.  Dental Calculus and the Evolution of the Human Oral Microbiome. , 2016, Journal of the California Dental Association.

[4]  Philip L. F. Johnson,et al.  Patterns of damage in genomic DNA sequences from a Neandertal , 2007, Proceedings of the National Academy of Sciences.

[5]  C. Warinner,et al.  HOPS: automated detection and authentication of pathogen DNA in archaeological remains , 2019, Genome Biology.

[6]  Sven Nahnsen,et al.  The nf-core framework for community-curated bioinformatics pipelines , 2020, Nature Biotechnology.

[7]  M. Meyer,et al.  Single-stranded DNA library preparation from highly degraded DNA using T4 DNA ligase , 2017, Nucleic acids research.

[8]  Heng Li,et al.  Minimap2: pairwise alignment for nucleotide sequences , 2017, Bioinform..

[9]  Heng Li.  Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM , 2013, 1303.3997.

[10]  C. Warinner,et al.  Salmonella enterica genomes from victims of a major sixteenth-century epidemic in Mexico , 2018, Nature Ecology & Evolution.

[11]  Bruce D. Smith,et al.  Early Allelic Selection in Maize as Revealed by Ancient DNA , 2003, Science.

[12]  Rob Knight,et al.  Insights from Characterizing Extinct Human Gut Microbiomes , 2012, PloS one.

[13]  Måns Magnusson,et al.  MultiQC: summarize analysis results for multiple tools and samples in a single report , 2016, Bioinform..

[14]  Janet Kelso,et al.  Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins , 2016, Nature.

[15]  Philip L. F. Johnson,et al.  mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters , 2013, Bioinform..

[16]  M. Hofreiter,et al.  Ancient DNA , 2019, Methods in Molecular Biology.

[17]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[18]  J. Krause,et al.  EAGER: efficient ancient genome reconstruction , 2016, Genome Biology.

[19]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[20]  J. Southon,et al.  Out of America: Ancient DNA Evidence for a New World Origin of Late Quaternary Woolly Mammoths , 2008, Current Biology.