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Abstract

The broadening utilisation of ancient DNA to address archaeological, palaeontological,and biological questions is resulting in a rising diversity in the size of laboratoriesand scale of analyses being performed. In the context of this heterogeneous landscape,we present an advanced, and entirely redesigned and extended version of the EAGERpipeline for the analysis of ancient genomic data. This Nextflow pipeline aims to addressthree main themes: accessibility and adaptability to different computing configurations,reproducibility to ensure robust analytical standards, and updating the pipeline tothe latest routine ancient genomic practices. The new version of EAGER has beendeveloped within the nf-core initiative to ensure high-quality software developmentand 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 beapplied by a diverse range of research groups and fields.