Pipelines (near publication)

These are pipelines we should publish soon. If you wish to use them, let us know and we can help you.

  • Eco-Flow/synteny - A pipeline that compares gene synteny between chromosome level genome assemblies. It takes genomes and gff (annotation) files and compares the macrosynteny using a variety of programs.

  • Eco-Flow/excon - A pipeline that runs gene family expansion and contraction analysis (via CAFE). This pipeline automates the analysis to run the basic steps in EXpansion and CONtraction of gene families, as well as running GO enrichment analysis on the output.

Pipelines in Development

  • Eco-Flow/pollen-metabarcoding - A pipeline to process meta barcoding data and assign species and produce tables/figures appropriate for this analysis.

Custom config files

  • Eco-Flow/configs - A repository to store custom configuration files we develop for our community.

Request a Pipeline

If you would like to request a pipeline then open a new GitHub Issue on our pipeline discussions repository.

Request a Feature

If you would like to request an additional feature to a published pipeline then please open a new issue on that pipeline’s GitHub repository.