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

Abstract

Rapid expansion of palaeo- and archaeogenomics is seeing an increasing diversity in the types of ancient DNA (aDNA) being studied. The scale of output and heterogeneity in the types of computational contexts and analyses being performed is correspondingly growing. We present a new version of the Efficient Ancient Genome Reconstruction pipeline (EAGER doi:10.1186/s13059-016-0918-z), which adapts to the challenges facing the rising utilisation of ancient DNA by the natural and social sciences. nf-core/eager expands the repertoire of tools to include increasingly routine analyses such as metagenomic screening for ancient microbes of interest and human biological sex-determination, while maintaining ease of use for those without computational backgrounds. A rewrite of the pipeline in the domain-specific-language Nextflow (doi:10.1038/nbt.3820) has been performed to allow portability and scalability across a wide range of computing environments, from personal computers to integration within High-Performance-Clusters (HPCs) and cloud platforms. nf-core/eager has also been developed within the nf-core community (doi:10.1101/610741) to enforce best-practice bioinformatics and software development guidelines. This helps to ensure accessibility for new contributors, continuous integration testing and feedback. Finally, nf-core/eager comes with extensive user-friendly, illustrated documentation which assists in the general understanding of NGS aDNA analysis for newcomers to the field. In this presentation, I will introduce the pipeline, encourage the greater community involvement to ensure long-term development and maintenance, and demonstrate how it will help democratise access and improve the quality of reproducible ancient DNA analysis for research groups of all sizes.

Date
May 2, 2021
Event
Location
Online
Toulouse

I presented a poster on the nf-core/eager pipeline.