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FooDMe 2

This is a pre-release

This pipeline performs processing of mitochondrial amplicon data to profile the composition of eukaryotic taxa.

Typical applications are in the analysis of food products, animal feed or seed materials.

FooDMe2 is a complete re-write of FooDMe with improved capabilities and portability. If you are migrating from FooDMe and are curious about the changes, you can read about them here.

A quick start guide can be found here. We do recommend you read the full documentation below, however.

Documentation

  1. What happens in this pipeline?
  2. Installation and configuration
  3. Running the pipeline
  4. Output
  5. Software
  6. Troubleshooting
  7. Developer guide

Acknowledgements

The FooDMe 2 team gratefully acknowledges the contributions made to FooDMe 1, by its (former) developers as well as the user community. We hope to continue this fruitful collaboration with FooDMe 2.

With our switch to Nextflow, we happily acknowledge the use of design principles and code snippets from the nf-co.re project, whose fundamental contributions to the Nextflow community has greatly influenced our work on FooDMe 2.