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Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager

View ORCID ProfileJames A. Fellows Yates, View ORCID ProfileThiseas C. Lamnidis, View ORCID ProfileMaxime Borry, View ORCID ProfileAida Andrades Valtueña, View ORCID ProfileZandra Fagernäs, View ORCID ProfileStephen Clayton, View ORCID ProfileMaxime U. Garcia, View ORCID ProfileJudith Neukamm, View ORCID ProfileAlexander Peltzer
doi: https://doi.org/10.1101/2020.06.11.145615
James A. Fellows Yates
1Microbiome Sciences Group, Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany; Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig Maximilian University, Munich, Germany • Funded by Max Planck Society
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Thiseas C. Lamnidis
2Population Genetics Group, Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany • Funded by Max Planck Society
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  • ORCID record for Thiseas C. Lamnidis
Maxime Borry
3Microbiome Sciences Group, Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany • Funded by Max Planck Society
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Aida Andrades Valtueña
4Computational Pathogenomics Group, Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany • Funded by Max Planck Society
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Zandra Fagernäs
5Microbiome Sciences Group, Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany • Funded by Max Planck Society
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Stephen Clayton
6Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany • Funded by Max Planck Society
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Maxime U. Garcia
7Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden • Funded by Barncancerfonden
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Judith Neukamm
8Palaeogenetics Group, Institute of Evolutionary Medicine, University of Zurich, Zürich, Switzerland
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Alexander Peltzer
9Quantitative Biology Center (QBiC), Eberhard-Karls-Universität, Tübingen, Germany; Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
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  • For correspondence: peltzer@shh.mpg.de
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Abstract

The broadening utilisation of ancient DNA to address archaeological, palaeontological, and biological questions is resulting in a rising diversity in the size of laboratories and scale of analyses being performed. In the context of this heterogeneous landscape, we present nf-core/eager, an advanced and entirely redesigned and extended version of the EAGER pipeline for the analysis of ancient genomic data. This Nextflow pipeline aims to address three main themes: accessibility and adaptability to different computing configurations, reproducibility to ensure robust analytical standards, and updating the pipeline to the latest routine ancient genomic practises. This new version of EAGER has been developed within the nf-core initiative to ensure high-quality software development and maintenance support; contributing to a long-term lifecycle for the pipeline. nf-core/eager will assist in ensuring that ancient DNA sequencing data can be used by a diverse range of research groups and fields.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Author affiliation updates. Various phrasing changes and descriptions of new functionality. Added new section: "Comparisons with other pipelines". Add supplemental files.

  • https://github.com/apeltzer/eager2-paper

  • https://apeltzer.github.io/eager2-paper/v/91f3ed63ce7115dab433adf550aa6f0f52ebcbf1/

  • https://github.com/nf-core/eager

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted October 21, 2020.
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Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager
James A. Fellows Yates, Thiseas C. Lamnidis, Maxime Borry, Aida Andrades Valtueña, Zandra Fagernäs, Stephen Clayton, Maxime U. Garcia, Judith Neukamm, Alexander Peltzer
bioRxiv 2020.06.11.145615; doi: https://doi.org/10.1101/2020.06.11.145615
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Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager
James A. Fellows Yates, Thiseas C. Lamnidis, Maxime Borry, Aida Andrades Valtueña, Zandra Fagernäs, Stephen Clayton, Maxime U. Garcia, Judith Neukamm, Alexander Peltzer
bioRxiv 2020.06.11.145615; doi: https://doi.org/10.1101/2020.06.11.145615

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