Introduction

Meta-omics methods aim to simultaneously analyse the entire multi-species potential and realised functional capacity of a biological sample. In other words to taxonomically and functionally characterise all organisms and their activity in a community.

The initial aims of this interest group will be:

  1. Helping coordinate compatibility between existing and potential meta-omic nf-core pipelines
  2. Implementing semi-‘chaining’ of sequential pipelines
  3. Developing standard parameters for different sub-disciplines (i.e. microbiome analysis) for each pipeline
  4. Documenting usage of ‘first level’ meta-omic pipelines (createtaxdb, ampliseq, eager, taxprofiler, mag, metatdenovo) followed by complementary analyses with “secondary” pipelines (e.g., funcscan, phageannotator, phyloplace, rnaseq, differentialabundance) etc.
Diagram showcasing how nf-core pipelines can potentially be used for complementary and sequential analysis within meta-omics disciplines using a London Underground style 'tube map'

Depending on interest/activity, other potential activities could include:

  1. Benchmarking meta-omic pipelines using relevant datasets (i.e. CAMI2), or reads generated using #readsimulator
  2. Adding nf-tests to meta-omic pipelines
  3. Reducing functional redundancy between pipelines

Activities

Initial activities will involve a monthly meeting with developers and users, to identify the most relevant problems related meta-omics with nf-core pipelines. Future activities may include presentations and discussions from topic-experts, as well as tutorials, workshops, and demo-days of nf-core pipelines.
  • Introduction