Integrated metagenomic data processing with nf-core

Metagenomics refers to techniques that aim to simultaneously analyze the DNA from all organisms in a sample. Given the ever-growing size of DNA datasets needed to address ecological questions, and the need to compare against a large number of genomes, Nextflow is an ideal framework for building scalable and computationally efficient pipelines. In this talk, I will introduce the nf-core offerings of community-developed pipelines for metagenomics. Of these, I will focus on pipelines for metagenomic taxonomic profiling (nf-core/taxprofiler), metagenomic de novo assembly (nf-core/mag), and screening for antimicrobial resistance and natural product genes (nf-core/funcscan). I will also discuss how these pipelines fit in the wider nf-core ecosystem, and how they can be utilised together for scientists in microbial ecology, clinical metagenomics, and even ancient DNA. Finally, I will briefly introduce the new 'meta-omics' nf-core special interest group and how we plan to further deepen the integration of the various nf-core metagenomics-related pipelines with upstream (e.g. nf-core/fetchngs) and downstream pipelines (e.g. nf-core/differentialabundance) to streamline primary metagenomic analysis.