New pipeline: nf-core/nanometabarcoding

Pipeline title/name

nanometabarcoding

Keywords

barcoding,nanopore

What is it about?

It takes raw Oxford Nanopore amplicon reads from a pooled, tagged metabarcoding run and produces a taxonomically annotated ASV table, to show which taxa are present in each sample and how many reads support each. Steps: NanoFilt filtering and NanoPlot QC → two-pass tag+primer demultiplexing with Cutadapt (forward tags, then matched reverse tags) → read clustering and consensus generation with amplicon_sorter → consensus polishing with Medaka → BLASTn against a user-supplied or locally built reference database → taxonomic assignment with taxonomizr, using percent-identity thresholds per rank and a last-common-rank consensus across hits, so ambiguous ASVs fall back to coarser ranks (rather than mis-assigning).

We (mostly Fernando Duarte) built this pipeline for a collaborator (https://github.com/Eco-Flow/nanoporemetabarcoding), keeping to the nf-core template, so should be an easy-ish convert.

We are not sure if this should be a separate workflow or a subworkflow on say nf-core/ampliseq. We are happy either, though our pipeline only shares one module in common with ampliseq, as nanopore data requires different tools in general. So I think it would be tidier if it was separate,,, but open to opinion here :)

We would love for this to move to nf-core now that it is established, and we are beginning to get a few users using it. Using nanopore makes this technique much more affordable, and it should get way more popular with easy tools to interpret the results (such as this pipeline).

Please provide a schematic diagram of the proposed pipeline

What would a minimal first release of this pipeline include?

We already have a fully working pipeline in https://github.com/Eco-Flow/nanoporemetabarcoding

So I think it would be just a case of going through a full review onto nf-core.

I confirm my proposed pipeline will follow nf-core guidelines. Most importantly, my pipeline will:

• be built with Nextflow.
• pass nf-core lint tests and use standardized parameters.
• be community-owned and developed within the nf-core organization.
• open source under the MIT license with proper credits and acknowledgments.
• have a descriptive, all lowercase, and without punctuation name.
• use the nf-core pipeline template and predominantly use official nf-core modules.
• focus on a specific data/analysis type with appropriate scope.
• have properly maintained documentation.
• be bundled using versioned Docker/Singularity containers.

Why do we need a new pipeline?

There is no pipeline to our knowledge that processes nanopore data from metabarcoding.

Who would be interested?

We already have a community using the pipeline (all biologists interested in agri-ecology), and did a workshop in Newcastle to 24 attendees from across Europe, so they can start using and testing the pipeline. We also have three publications lined up, which I hope will drive interest in this analysis type.

https://eco-flow.github.io/events/2026-07-21-nanometabarcoding-newcastle/

What has been done so far

https://github.com/Eco-Flow/nanoporemetabarcoding

The pipeline is ready, there are just some post processing, maybe some nice figures we could add on the end. Once we get this through first release, we hope that people will start suggesting changes and improvements.

URL to existing work (if applicable)

No response

Are there any similar existing nf-core pipelines?

ampliseq

Start by reviewing the existing implementation in Eco-Flow/nanoporemetabarcoding and compare it with the nf-core pipeline template and ampliseq. Resolve whether this should be a standalone workflow or subworkflow, then identify the migration, post-processing, documentation, and review work needed. Done means a reviewed nf-core pipeline that passes the stated guidelines and is ready for its first release.