EAGER: efficient ancient genome reconstruction
Open accessAbstract
BACKGROUND: The automated reconstruction of genome sequences in ancient genome analysis is a multifaceted process. RESULTS: Here we introduce EAGER, a time-efficient pipeline, which greatly simplifies the analysis of large-scale genomic data sets. EAGER provides features to preprocess, map, authenticate, and assess the quality of ancient DNA samples. Additionally, EAGER comprises tools to genotype samples to discover, filter, and analyze variants. CONCLUSIONS: EAGER encompasses both state-of-the-art tools for each step as well as new complementary tools tailored for ancient DNA data within a single integrated solution in an easily accessible format.
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Pipelines like EAGER2 integrate WGA tools with other bioinformatics software, providing a comprehensive solution for genomic analysis.
“For example, pipelines like EAGER2 integrate WGA tools with other bioinformatics software, providing a comprehensive solution for genomic analysis [73].”
From Whole-Genome Alignment: Methods, Challenges, and Future Directions (2024) · cites this paper as [73]
The Implementation section describes EAGER as an integrated pipeline combining read-mapping, genotyping, and other bioinformatics tools for genomic analysis. It does not describe EAGER2 or identify any WGA tools in the pipeline, so those specific parts of the claim are unsupported. (LLM, conf=0.88)
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- Authors
- Peltzer, A., Jäger, G., Herbig, A., Seitz, A., Kniep, C., Krause, J., & Nieselt, K.
- Affiliations
- Max Planck Institute of Geoanthropology (DE)
- University of Tübingen (DE)
- Senckenberg Centre for Human Evolution and Palaeoenvironment (DE)
- Corresponding author
- Peltzer, Alexander
- Venue
- Genome Biology
- Published
- 2016-03-31
- Volume
- 17
- Issue
- 1
- Pages
- 60-60
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC4815194
- OpenAlex
- W2319185332
- Cited by
- 509
- References
- 10
- Citations by year
- 2026: 79 · 2025: 77 · 2024: 51 · 2023: 49 · 2022: 57 · 2021: 54 · 2020: 48 · 2019: 34 · 2018: 33 · 2017: 14 · 2016: 11
- FWCI
- 20.57
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- Genome biology (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion, cc-by)
- Informationszentrum Lebenswissenschaften (ZB MED) (submittedVersion, cc-by)
- MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
- Funders
- Eberhard Karls Universität Tübingen
- Max-Planck-Institut für Menschheitsgeschichte
- 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, genome reconstruction, variant calling, variant filtering, genome mapping, DNA authentication, bioinformatics pipeline, large-scale genomic data
- MeSH terms
- Chromosome Mapping, Fossils, Software, Genome, Sequence Analysis, DNA, Workflow
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