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

doi:10.7717/peerj.10947

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

PeerJ. 2021 Mar 16:9:e10947. doi: 10.7717/peerj.10947. eCollection 2021.

Authors

James A Fellows Yates^{1

2}, Thiseas C Lamnidis¹, Maxime Borry¹, Aida Andrades Valtueña¹, Zandra Fagernäs¹, Stephen Clayton¹, Maxime U Garcia^{3

4}, Judith Neukamm^{5

6}, Alexander Peltzer^{1

7}

Affiliations

¹ Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.
² Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität München, Münich, Germany.
³ National Genomics Infrastructure, Science for Life Laboratory, Stockholm, Sweden.
⁴ Barntumörbanken, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.
⁵ Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland.
⁶ Institute for Bioinformatics and Medical Informatics, Eberhard-Karls University Tübingen, Tübingen, Germany.
⁷ Quantitative Biology Center, Eberhard-Karls University Tübingen, Tübingen, Germany.

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 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 practices. The 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 life-cycle for the pipeline. nf-core/eager will assist in ensuring that a wider range of ancient DNA analyses can be applied by a diverse range of research groups and fields.

Keywords: Ancient DNA; Bioinformatics; Genomics; Metagenomics; Nextflow; Palaeogenomics; Pipeline; Reproducibility.

Grants and funding

James A. Fellows Yates, Thiseas C. Lamnidis., Maxime Borry, Aida Andrades Valtueña, Zandra Fagernäs, and Stephen Clayton were supported by the Max Planck Society. James A. Fellows Yates was supported by the ERC Starting Grant project FoodTransforms (ERC-2015-StG 678901-Food-Transforms) funded by the European Research Council awarded to Philipp W. Stockhammer (Ludwig Maximilian University, Munich). Thiseas C. Lamnidis was supported by the European Union’s Horizon 2020 research and innovation programme (grant agreement No 851511) with the ERC Starting Grant project MICROSCOPE funded by the European Research Council awarded to Stephan Schiffels (Max Planck Institute for the Science of Human History). Zandra Fagernäs was supported by the Werner Siemens Stiftung funded project ‘Paleobiotechnology’ awarded to Christina Warinner (Max Planck Institute for the Science of Human History). Maxime U. Garcia is supported by the BarncancerFonden. There was no additional external funding received for this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.