Pipelines
Our main Eco-Flow contributed pipelines. Those on github.com/Eco-Flow are built on a Nextflow/nf-core framework for specific research projects; those on github.com/nf-core follow the stricter nf-core guidelines for the wider community. Some pipelines stay private until their paper is published.
Released
Automated gene family expansion & contraction analysis with CAFE5, plus GO enrichment.
Process pollen metabarcoding data with VSEARCH and assign species to barcodes.
Assess genome assembly and annotation quality with an ensuite of tools, plus phylogeny.
In development
Compare gene macrosynteny between chromosome-level genome assemblies.
Process and annotate nanopore metabarcoding data across taxonomic levels.
Compare transposable element (TE) content across genomes.
Early development
Projects we support
External projects we advise on or help develop. These are not Eco-Flow pipelines — they're built and maintained by their own teams, and we provide Nextflow and nf-core guidance.
A Nextflow/nf-core workflow for genome assembly from short-read sequencing data — covering pre-processing, assembly and quality control. Developed by the Fungarium team at Kew, with our Nextflow/nf-core guidance.
External · we adviseA Nextflow pipeline that produces consensus protein-domain annotations for protein structures, combining the Chainsaw, Merizo and UniDoc domain parsers.
External · we adviseCustom config files
Want to run our pipelines — or any nf-core pipeline — on your HPC or institutional cluster? We can help build a custom Nextflow configuration file so everything runs smoothly on your infrastructure.