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


Fellows Yates, James A; Lamnidis, Thiseas C; Borry, Maxime; Andrades Valtueña, Aida; Fagernäs, Zandra; Clayton, Stephen; Garcia, Maxime U; Neukamm, Judith; Peltzer, Alexander (2021). Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager. PeerJ, 9:e10947.

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.

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.

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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:04 Faculty of Medicine > Institute of Evolutionary Medicine
Dewey Decimal Classification:610 Medicine & health
Scopus Subject Areas:Life Sciences > General Neuroscience
Life Sciences > General Biochemistry, Genetics and Molecular Biology
Life Sciences > General Agricultural and Biological Sciences
Uncontrolled Keywords:General Biochemistry, Genetics and Molecular Biology, General Neuroscience, General Agricultural and Biological Sciences, General Medicine
Language:English
Date:16 March 2021
Deposited On:27 Apr 2021 13:51
Last Modified:01 May 2021 21:21
Publisher:PeerJ, Ltd.
ISSN:2167-8359
OA Status:Gold
Free access at:PubMed ID. An embargo period may apply.
Publisher DOI:https://doi.org/10.7717/peerj.10947
PubMed ID:33777521
Project Information:
  • : FunderH2020
  • : Grant ID851511
  • : Project TitleMICROSCOPE - Zooming into the Population History of Iron Age Europe with Rare Genetic Variants.

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