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

Autor:	Fellows Yates JA; Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.; Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität München, Münich, Germany., Lamnidis TC; Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany., Borry M; Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany., Andrades Valtueña A; Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany., Fagernäs Z; Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany., Clayton S; Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany., Garcia MU; National Genomics Infrastructure, Science for Life Laboratory, Stockholm, Sweden.; Barntumörbanken, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden., Neukamm J; Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland.; Institute for Bioinformatics and Medical Informatics, Eberhard-Karls University Tübingen, Tübingen, Germany., Peltzer A; Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.; Quantitative Biology Center, Eberhard-Karls University Tübingen, Tübingen, Germany.
Jazyk:	angličtina
Zdroj:	PeerJ [PeerJ] 2021 Mar 16; Vol. 9, pp. e10947. Date of Electronic Publication: 2021 Mar 16 (Print Publication: 2021).
DOI:	10.7717/peerj.10947
Abstrakt:	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. Competing Interests: The authors declare there are no competing interests. (©2021 Fellows Yates et al.)
Databáze:	MEDLINE
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