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

Fellows Yates, J. A., Lamnidis, T. C., Borry, M., Andrades Valtueña, A., Fagernäs, Z., Clayton, S., et al. (2021). Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager. PeerJ, e10947. doi:10.7717/peerj.10947.

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zip. - (last seen: March 2021)
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nf-core/eager: [2.3.1] - Aalen (Patch) - 2021-01-14 (Version 2.3.1). - (last seen: March 2021)

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 Creators:
Fellows Yates, James A.1, Author              
Lamnidis, Thiseas Christos1, Author              
Borry, Maxime1, Author              
Andrades Valtueña, Aida1, Author              
Fagernäs, Zandra1, Author              
Clayton, Stephen1, Author              
Garcia, Maxime U., Author
Neukamm, Judith, Author
Peltzer, Alexander1, Author              
Affiliations:
1Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society, ou_2074310              

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Free keywords: Bioinformatics, Palaeogenomics, Ancient DNA, Pipeline, Nextflow, Reproducibility, Genomics, Metagenomics
 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 StatementThe authors have declared no competing interest.

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Language(s): eng - English
 Dates: 2021-03-16
 Publication Status: Published online
 Pages: 25
 Publishing info: -
 Table of Contents: Introduction
Materials and methods
- Updated Workflow
- Usage
- Benchmarking
-- Functionality demonstration
-- Run-time comparison
Results
- Functionality demonstration
- Run-time comparison
Discussion
Conclusion
 Rev. Type: Peer
 Identifiers: DOI: 10.7717/peerj.10947
DOI: 10.1101/2020.06.11.145615
Other: shh2776
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Title: PeerJ
  Other : PeerJ
Source Genre: Journal
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Publ. Info: London [u.a.] : PeerJ Inc.
Pages: - Volume / Issue: - Sequence Number: e10947 Start / End Page: - Identifier: ISSN: 2167-8359
CoNE: https://pure.mpg.de/cone/journals/resource/2167-8359

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Title: bioRxiv
Source Genre: Journal
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Publ. Info: Cold Spring Harbor : Cold Spring Harbor Laboratory
Pages: - Volume / Issue: - Sequence Number: 145615 Start / End Page: - Identifier: URI: https://www.biorxiv.org/