An efficient pipeline for ancient DNA mapping and recovery of endogenous ancient DNA from whole-genome sequencing data
Open accessAbstract
Ancient DNA research has developed rapidly over the past few decades due to improvements in PCR and next-generation sequencing (NGS) technologies, but challenges still exist. One major challenge in relation to ancient DNA research is to recover genuine endogenous ancient DNA sequences from raw sequencing data. This is often difficult due to degradation of ancient DNA and high levels of contamination, especially homologous contamination that has extremely similar genetic background with that of the real ancient DNA. In this study, we collected whole-genome sequencing (WGS) data from 6 ancient samples to compare different mapping algorithms. To further explore more effective methods to separate endogenous DNA from homologous contaminations, we attempted to recover reads based on ancient DNA specific characteristics of deamination, depurination, and DNA fragmentation with different parameters. We propose a quick and improved pipeline for separating endogenous ancient DNA while simultaneously decreasing homologous contaminations to very low proportions. Our goal in this research was to develop useful recommendations for ancient DNA mapping and for separation of endogenous DNA to facilitate future studies of ancient DNA.
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Xu et al. find that BWA-MEM works best for aDNA with parameters -k 19 -r 2.5.
“while Xu et al. find that BWA-MEM works best for aDNA with parameters -k 19 -r 2.5 [11]”
From <tt>SAFARI</tt> : pangenome alignment of ancient DNA using purine/pyrimidine encodings (2025) · cites this paper as [11]
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References 39 · Cited by 20
- Authors
- Xu, W., Lin, Y., Zhao, K., Li, H., Tian, Y., Ngatia, J. N., Ma, Y., Sahu, S. K., Guo, H., Guo, X., Xu, Y. C., Liu, H., Kristiansen, K., Lan, T., & Zhou, X.
- Affiliations
- Chinese Academy of Sciences (CN)
- BGI Group (China) (CN)
- Northeast Forestry University (CN)
- Forest Inventory and Planning Institute of Jilin Province Changchun China
- College of Wildlife Resources Northeast Forestry University Harbin China
- Corresponding author
- Zhou, Xinying
- ORCID
- Venue
- Ecology and Evolution
- Publisher
- Wiley
- Published
- 2020-12-21
- Volume
- 11
- Issue
- 1
- Pages
- 390-401
- ISSN
- 2045-7758 (ISSN-L)
- PMC
- PMC7790629
- OpenAlex
- W3114070225
- Cited by
- 20
- References
- 39
- Citations by year
- 2026: 4 · 2025: 4 · 2024: 4 · 2022: 3 · 2021: 4 · 2020: 1
- FWCI
- 1.17
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Ecology and Evolution (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, other-oa)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Chinese Academy of Sciences (26000000, XDB26000000)
- Government of Jiangxi Province
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- ancient DNA, read mapping, deamination, depurination, DNA fragmentation
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