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

• DOI: 10.1101/2020.06.11.145615
• Publication Date: 2020-06-15T15:15:49Z
• Authors: James A. Fellows ...; Thiseas C. Lamnidis; Maxime Borry; Aida Andrades Val...; Zandra Fagernäs; Stephen Clayton; Maxime U. Garcia; Judith Neukamm; Alexander Peltzer
• Keywords: 0301 basic medicine; Bioinformatics; QH301-705.5; 0206 medical engineering; 610 Medicine & health; Genetics and Molecular Biology; 1100 General Agricultural and Biological Sciences; 02 engineering and technology; 03 medical and health sciences; 1300 General Biochemistry, Genetics and Molecular Biology; Pipeline; Biology (General); Palaeogenomics; Ancient DNA; General Neuroscience; R; 2800 General Neuroscience; General Medicine; Reproducibility; Nextflow; Anthropology; 11294 Institute of Evolutionary Medicine; General Biochemistry; Medicine; General Agricultural and Biological Sciences

AbstractThe 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.