LongTermStorageaDNA Pipeline (ongoing Project) 🔬

LongTermstoragePipeline is a pipeline that I am currently developing with the aim to create, from the scripts I developed to analyse the data from my master’s thesis into a reproducible (and easy to use) pipeline.

This Pipeline will enable the user (once it is finalised) to analyse following characteristics of aDNA samples: Preprocessing of samples with aDNAPrePro: finished v1.1 (programs: Cutadapt, SAMtools, bwa), authentication and deamination rates (program: MapDamage), contamination kinship analysis (program: TKGWV2), Read length calculation (program: Amber ).

A bioinformatics pipeline for the analysis of ancient DNA (aDNA) samples.

This pipeline contains a set of scripts and customized code, which were originally developed for the analysis of ancient human genomic data generated for the project: “The effect of long-term storage on ancient DNA samples” (Master’s thesis).

Thesis available here: https://utheses.univie.ac.at/detail/74668

As of now (March 2026) I have finished the first module (aDNAPrePro).

aDNAPrePro (first finished and available module):

The first part of the pipeline, aDNAPrePro (v1.1), is now available. The pipeline aDNAPrePro (V1.1) preprocesses aDNA samples.

Installation

Instructions on Installation are available on the README at the GitHub project website:

https://github.com/raimo-al/LongTermStorageaDNA

Citation:

Please cite https://utheses.univie.ac.at/detail/74668 if you use this pipeline.

LongTermStorageaDNA-Scripts is available under the terms of the MIT license.

The computational results of this work have been achieved using the University of Vienna`s Life Science Compute Cluster (LiSC).

Additional references include:

Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. journal, 17(1), 10-12.

bwa Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics , 25(14), 1754–1760. https://doi.org/10.1093/bioinformatics/btp324. Download: http://bio-bwa.sourceforge.net/bwa.shtml

SAMtools Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., … 1000 Genome Project Data Processing Subgroup. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics , 25(16), 2078–2079. https://doi.org/10.1093/bioinformatics/btp352. Download: http://www.htslib.org/

Fernandes, DM, Cheronet, O, Gelabert, P, Pinhasi, R. TKGWV2: an ancient DNA relatedness pipeline for ultra-low coverage whole genome shotgun data. Sci Rep 11, 21262 (2021). https://doi.org/10.1038/s41598-021-00581-3

Dolenz, S., van der Valk, T., Jin, C., Oppenheimer, J., Sharif, M. B., Orlando, L., … & Heintzman, P. D. (2024). Unravelling reference bias in ancient DNA datasets. Bioinformatics, 40(7), btae436.

Ginolhac, A., Rasmussen, M., Gilbert, M. T. P., Willerslev, E., & Orlando, L. (2011). mapDamage: testing for damage patterns in ancient DNA sequences. Bioinformatics, 27(15), 2153-2155.

Briggs, A. W., Stenzel, U., Johnson, P. L., Green, R. E., Kelso, J., Prüfer, K., … & Pääbo, S. (2007). Patterns of damage in genomic DNA sequences from a Neandertal. Proceedings of the National Academy of Sciences, 104(37), 14616-14621.

Contact:

If you have any question about my research or the project please feel free to contact me at: alexandra.raimo@protonmail.com or alexandra.raimo@univie.ac.at .