Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager
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 r...
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| Format: | Article |
| Language: | English |
| Published: |
PeerJ Inc.
2021-03-01
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| Series: | PeerJ |
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| Online Access: | https://peerj.com/articles/10947.pdf |
| _version_ | 1827611440640425984 |
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| author | James A. Fellows Yates Thiseas C. Lamnidis Maxime Borry Aida Andrades Valtueña Zandra Fagernäs Stephen Clayton Maxime U. Garcia Judith Neukamm Alexander Peltzer |
| author_facet | James A. Fellows Yates Thiseas C. Lamnidis Maxime Borry Aida Andrades Valtueña Zandra Fagernäs Stephen Clayton Maxime U. Garcia Judith Neukamm Alexander Peltzer |
| author_sort | James A. Fellows Yates |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-09T08:06:17Z |
| format | Article |
| id | doaj.art-3c8696d96976438da267066c08f9db01 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T08:06:17Z |
| publishDate | 2021-03-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-3c8696d96976438da267066c08f9db012023-12-02T23:47:46ZengPeerJ Inc.PeerJ2167-83592021-03-019e1094710.7717/peerj.10947Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eagerJames A. Fellows Yates0Thiseas C. Lamnidis1Maxime Borry2Aida Andrades Valtueña3Zandra Fagernäs4Stephen Clayton5Maxime U. Garcia6Judith Neukamm7Alexander Peltzer8Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, GermanyDepartment of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, GermanyDepartment of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, GermanyDepartment of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, GermanyDepartment of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, GermanyDepartment of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, GermanyNational Genomics Infrastructure, Science for Life Laboratory, Stockholm, SwedenInstitute of Evolutionary Medicine, University of Zurich, Zurich, SwitzerlandDepartment of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, GermanyThe 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.https://peerj.com/articles/10947.pdfBioinformaticsPalaeogenomicsAncient DNAPipelineNextflowReproducibility |
| spellingShingle | James A. Fellows Yates Thiseas C. Lamnidis Maxime Borry Aida Andrades Valtueña Zandra Fagernäs Stephen Clayton Maxime U. Garcia Judith Neukamm Alexander Peltzer Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager PeerJ Bioinformatics Palaeogenomics Ancient DNA Pipeline Nextflow Reproducibility |
| title | Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager |
| title_full | Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager |
| title_fullStr | Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager |
| title_full_unstemmed | Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager |
| title_short | Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager |
| title_sort | reproducible portable and efficient ancient genome reconstruction with nf core eager |
| topic | Bioinformatics Palaeogenomics Ancient DNA Pipeline Nextflow Reproducibility |
| url | https://peerj.com/articles/10947.pdf |
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