---
# System prepended metadata

title: 'sig proposal: metagenomics/microbial ecology'
tags: [proposal, sig, sig-proposals, meta-omics]

---

 # 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, 
