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

PeerJ

卷:9

Alexander Peltzer¹  Thiseas C. Lamnidis¹  Maxime Borry¹  James A. Fellows Yates¹  Aida Andrades Valtueña¹  Zandra Fagernäs¹  Stephen Clayton¹  Judith Neukamm²  Maxime U. Garcia³ 

[1] Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany;

[2] Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland;

[3] National Genomics Infrastructure, Science for Life Laboratory, Stockholm, Sweden;

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

DOI  :  10.7717/peerj.10947

来源: DOAJ

【 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】

Unknown