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

PeerJ

article

James A. Fellows Yates¹  Thiseas C. Lamnidis¹  Maxime Borry¹  Aida Andrades Valtueña¹  Zandra Fagernäs¹  Stephen Clayton¹  Maxime U. Garcia³  Judith Neukamm⁵  Alexander Peltzer¹ 

[1] Department of Archaeogenetics, Max Planck Institute for the Science of Human History;Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität München;National Genomics Infrastructure, Science for Life Laboratory;Barntumörbanken, Department of Oncology-Pathology, Karolinska Institutet;Institute of Evolutionary Medicine, University of Zurich;Institute for Bioinformatics and Medical Informatics, Eberhard-Karls University Tübingen;Quantitative Biology Center, Eberhard-Karls University Tübingen

关键词: Bioinformatics;    Palaeogenomics;    Ancient DNA;    Pipeline;    Nextflow;    Reproducibility;    Genomics;    Metagenomics;   

DOI  :  10.7717/peerj.10947

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

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.

【 授权许可】

CC BY