# SIG proposal: metagenomics/microbial ecology ## Brainstorm **Proposal activities:** - Coordinating cross-pipeline compatibility (samplesheet output/input) - Gold-standard sets of parameters (e.g. clinicial metagenomics) [e.g. https://github.com/nf-core/mag/issues/455#issuecomment-1589356543] - Recommendations/tutorials for downstream analysis of pipeline results (What do I do with a community table/a MAG?) - Compile lists publications utilizing various approaches as examples. - Establish use-cases for certain approaches (e.g. When is nf-core/mag appropriate? What are the strengths and weaknesses of *de novo* assembly?) - Benchmarking pipelines with nf-core/readsimulator? (*This could be difficult/unreasonable, but I'm just throwing it out there!*) - Maybe also benchmark (relevant) pipelines against CAMI2 dataset? - Adding nf-test to relevant pipelines? :grimacing: - Reducing functionality redundency **Potential SIG Names:** - microbial communities - microbial omics - metagenomics excludes amplicons and transcriptiomics - community genomics - community omics - microbial diversity? (and function?) **Discussions:** - https://nfcore.slack.com/archives/CE9MS66BS/p1712226146333839 **Possible (co)leads:** - James F.Y. - Carson M. - Daniel L. - Jim D. (in a few months?) **Posts:** - https://nfcore.slack.com/archives/C02K5GX2W93/p1712226154096869 - https://nfcore.slack.com/archives/C02FC6VFQG1/p1712226169560849 - https://nfcore.slack.com/archives/CE9MS66BS/p1712226146333839 - https://nfcore.slack.com/archives/C062H82UCRG/p1712226157913549 **Relevant pipelines:** - ampliseq - metatdenovo - detaxizer - funcscan - eager - mag - taxprofiler - bacass - createtaxdb - phageannotator - magmap - readsimulator? (for benchmarking?) - phyloplace (protein classification, phylogenetic placement of organisms) - viralrecon - rnaseq & differentialabudance (more specialized: magmap) - bacass (simple microbial isolate genome assembly) Potential Pipeline relationship: ```mermaid flowchart TD inputreads([input reads]) -.fastqs.-> taxprofiler inputfasta([reference genomes]) --fastas--> createtaxdb inputfasta([reference genomes]) --fastas & gffs--> rnaseq fetchngs --public reads-->inputreads fetchngs --> amplicons createtaxdb --databases--> taxprofiler inputreads --fastqs--> eager inputreads --fastqs-->mag inputreads --fastqs-->rnaseq taxprofiler --processed reads--> mag mag -. processed reads .-> taxprofiler mag --contigs--> funcscan mag --contigs & reads--> phageannotator mag --fastas-->createtaxdb mag --fastas & gffs--> magmap mag --fastas & gffs--> rnaseq rnaseq-->differentialabundance inputreads([input reads])--> metatdenovo amplicons([amplicon reads])--> ampliseq metatdenovo --fastas--> funcscan metatdenovo --fastas--> phyloplace metatdenovo --fastas--> phageannotator mag --fastas--> phyloplace inputfasta--fastas--> magmap inputfasta--reference genomes-->eager createtaxdb --databases--> eager inputreads([input reads])--> magmap inputfasta-->mag inputfasta-->taxprofiler ``` ## Official Proposal ### Interest group name Community 'omics ### What is it about? Meta-omics methods aim to simultaneously analyse the entire 'omic' content of a biological sample, in other words to charactise all organisms (and their acitivity) within a given context. The aims of this interest group will be to help coordinate compatibility between current and existing meta\*omic nf-core pipelines. Proposed objectives include coordinating semi-'chaining' of pipelines, developing standard parameters for different sub-disciplines for each pipeline, and documentation utilising 'first level' meta\*omic pipelines, with complementary 'secondary' analysis, e.g. funcscan, phageannotator, phyloplace, rnaseq etc. ### Keywords metagenomics, metataxonomics, metatranscriptomics, microbial ecology, clinical metagenomics ## Lead contact person James Fellows Yates, Carson Miller, Daniel Lundin ## Pre-existing participating consortia (if relevant) None ## List of typical nf-core pipelines used #ampliseq, #createtaxdb, #eager, #mag, #magmap, #metatdenovo, #taxprofiler,