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.

Ready to use

Released

Eco-Flow/excon

Automated gene family expansion & contraction analysis with CAFE5, plus GO enrichment.

Released

Eco-Flow/synteny

Compare gene macrosynteny between chromosome-level genome assemblies.

Released

Eco-Flow/pollen-metabarcoding

Process pollen metabarcoding data with VSEARCH and assign species to barcodes.

Released

Functional & close to release

In development

Eco-Flow/nanoporemetabarcoding

Process and annotate nanopore metabarcoding data across taxonomic levels.

In development

nf-core/genomeqc

Assess genome assembly and annotation quality with an ensuite of tools, plus phylogeny.

In development

Early stage

Early development

nf-core/gwas

Conduct genome-wide association studies (GWAS) with plink.

Early development

Collaborations

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.

FSP Assembly Pipeline ↗

Royal Botanic Gardens, Kew

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 advise

Request a pipeline

Open an issue on our pipeline discussions repository, or email us.

ecoflow.ucl@gmail.com

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Custom 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.

ecoflow.ucl@gmail.com