EAGER

EAGER (efficient ancient genome reconstruction) is a software pipeline to reconstruct ancient genomes and analyze large genomic datasets. The EAGER package includes tools for preprocessing, filtering, variant analysis, authenticating, mapping, genotyping, and quality assessment.

Topic

Genomics;Evolutionary biology;Population genetics;Phylogenetics

Detail

  • Operation: Phylogenetic tree reconstruction

  • Software interface: Command-line user interface

  • Language: Shell;Java;Python

  • License: The MIT License

  • Cost: Free

  • Version name: 2.4.5

  • Credit: The Max Planck Society, ERC Starting Grant project FoodTransforms funded by the European Research Council, the European Union’s Horizon 2020 research and innovation programme with the ERC Starting Grant project MICROSCOPE funded by the European Research Council, the Werner Siemens Stiftung funded project ‘Paleobiotechnology’, the BarncancerFonden, Deutsche Forschungsgemeinschaft, the University of Tübingen.

  • Input: -

  • Output: -

  • Contact: alexander.peltzer@uni-tuebingen.de

  • Collection: -

  • Maturity: Mature

Publications

  • The nf-core framework for community-curated bioinformatics pipelines.
  • Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, et al. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol 38(3): 276-278.
  • https://doi.org/10.1038/s41587-020-0439-x
  • PMID: 32055031
  • PMC: -
  • EAGER: efficient ancient genome reconstruction.
  • Peltzer A, Jäger G, Herbig A, Seitz A, Kniep C, Krause J, Nieselt K. EAGER: efficient ancient genome reconstruction. Genome Biol. 2016 Mar 31;17:60. doi: 10.1186/s13059-016-0918-z. PMID: 27036623; PMCID: PMC4815194.
  • https://doi.org/10.1186/s13059-016-0918-z
  • PMID: 27036623
  • PMC: PMC4815194
  • Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager.
  • Fellows Yates JA, Lamnidis TC, Borry M, Andrades Valtueña A, Fagernäs Z, et al. (2021). Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager. PeerJ 9: e10947.
  • https://doi.org/10.7717/peerj.10947
  • PMID: 33777521
  • PMC: PMC7977378

Download and documentation

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