As ancient metagenomics becomes more popular and techniques advance, the amount of data that needs to be processed will get larger and larger. Efficiently processing such data is not only an issue for the primary researcher, but also for reproducible science - allowing other researchers to check the results of previous publications as well as incorporate this data into their own research. nf-core/eager is a user-friendly and flexible dedicated ancient DNA (meta)genomics screening pipeline. It follows current established ‘best practices’ for processing aDNA data and employs Nextflow to allow portability across different computing infrastructures (from laptops to HPC clusters) facilitating reproducible analyses. In this talk I will demonstrate the metagenomic and microbial genomic capability of the pipelines. I will show the different functionalities of the pipeline that allow for taxonomic screening and authentication of both multi-species communities such as microbiomes, and also modules that are particularly relevant for both phylogenetic and functional downstream genomics analyses of microbes such as pathogens.
I presented on the nf-core/eager pipeline, in the session ‘Tools up or Die - gaps and solutions in ancient metagenomics analysis’ organised and chaired by Aida Andrades Valtueña.