Nextflow pipelines from EPI2ME

This is a joint blog post by Chris Wright of Oxford Nanopore Technologies and Paolo Di Tommaso of Seqera.

Introduction

Besides the well-known nf-core, there are several collections of high-quality Nextflow pipelines and modules, including:

• Nextflow pipelines from the International Agency for Research on Cancer (IARC)
• Various pipelines and Nextflow modules maintained by UMCU Genetics
• QBiC pipelines maintained at the University of Tübingen

We thought it was high time that we gave some attention to EPI2ME™ Workflows - another set of professionally maintained pipelines developed by the EPI2ME team at Oxford Nanopore Technologies (ONT).

In this article, we discuss the workflows, compare them to similar pipelines from nf-core, and explain how users can easily get started using software from EPI2ME™ or the Seqera Platform.

About Oxford Nanopore

Oxford Nanopore Technologies was founded in 2005 as a spin-off from the University of Oxford in the UK. The company has developed, commercialized, and continues to innovate on a new generation of sensing technology that uses nanopores - nano-scale holes - embedded in high-tech electronics to perform comprehensive analyses of single molecules.

Oxford Nanopore’s first products sequence DNA and RNA. The technology offers scalability from portable to ultra-high throughput formats that are appropriate for broad use. This combines with real-time data delivery for rapid insights and dynamic workflows, and PCR-free sequencing of any length of fragment for the ability to accurately characterize biological variation.

Today, Oxford Nanopore offers a range of products, from laboratory preparation and automation solutions to sequencers to software tools for analysis, in addition to industry-leading sequencing products, which range from the portable MinION™ sequencer to benchtop GridION™ devices with integrated compute to their high-throughput PromethION™ series with up to 48 independently addressable flow cells.

EPI2ME

The EPI2ME team within Oxford Nanopore is composed of a dozen people with expertise in diverse fields, from genetics to computational biology and focus on a variety of workflows from microbiology to clinical research applications. EPI2ME provides Oxford Nanopore’s open-source bioinformatics platform and develops and maintains pipelines tailored to nanopore sequencing data.

In addition to maintaining Nextflow pipelines, the EPI2ME team also supports:

• Oxford Nanopore’s Open Data provided through the registry of open data on AWS.
• The EPI2ME desktop application for Windows, Mac and Linux for running workflows locally or in the cloud.
• Various tutorials and training materials for bioinformaticians.

Meet the pipelines

The EPI2ME team selected Nextflow as their preferred framework for workflows in March of 2021. The pipelines are written using both community provided and bespoke (open-source) tools and maintained by a dedicated team of professional bioinformaticians and software developers. They are extensively documented, and generate high-quality interactive reports.

The pipelines are freely available from GitHub and are grouped based on their functionality as follows:

• Pipelines for handling basic tasks such as base calling and alignment: wf-basecalling and wf-alignment
• Pipelines for studying human genetics and cancer: wf-human-variation and wf-somatic-variation
• Pipelines for genome assembly: wf-clone-validation and wf-bacterial-genomes
• Metagenomic analysis pipelines: wf-metagenomics and wf-16s
• Direct RNA sequencing and cDNA: wf-transcriptomes and wf-single-cell
• Pipelines for infectious disease including SARS-CoV-2, Monkeypox, Influenza, and tuberculosis: wf-artic, wf-mpx, wf-flu, and wf-tb-amr
• Targeted sequencing pipelines: wf-amplicon
• Other pipelines: wf-pore-c, wf-aav-qc

While the pipelines pre-date some recent nf-core practices, EPI2ME pipelines are DSL2 compliant, modular, and employ their own consistent coding standards. Like nf-core, EPI2ME provides a standard template that can be used as the basis for developing new workflows. Community-developed workflows following those standards can be easily integrated in the EPI2ME desktop application, increasing accessibility for other Oxford Nanopore users, through an intuitive graphical interface. The EPI2ME team also publishes the containers for each workflow on Docker Hub and makes them freely available.

Running the EPI2ME pipelines

For each pipeline, instructions are provided for running:

• From the command line
• On the Seqera Platform
• Using the EPI2ME desktop application
  
  

EPI2ME pipelines on Seqera Platform

Since EPI2ME pipelines include a nextflow_schema.json file, pipelines can be adapted for use with the Seqera Platform, leveraging Seqera’s interactive interface for launching and monitoring pipelines in their preferred HPC or cloud computing environment.

Seqera users can simply add EPI2ME pipelines to the Seqera Launchpad via Seqera Pipelines or by pointing to the EPI2ME GitHub repo and selecting a pipeline version.

After adding a tile for the EPI2ME pipeline in Seqera, users can launch pipelines to their preferred compute environments, monitor execution, and share resulting datasets and pipeline results.

EPI2ME pipelines using EPI2ME Desktop Application

Users can learn more about installing the EPI2ME desktop application here. This desktop tool uses Nextflow and Docker to run bioinformatics workflows and provides an intuitive, easy-to-use interface. With the EPI2ME desktop application, users can launch EPI2ME workflows and other Nextflow pipelines from their choice of desktop environment including Windows (via Windows Subsystem for Linux, WSL), MacOS, or Linux.

Conclusion

EPI2ME provides a comprehensive and valuable collection of Nextflow pipelines developed and made available by Oxford Nanopore, catering to a wide range of bioinformatics use cases. These pipelines can be deployed on both Seqera Platform and the EPI2ME Desktop application.

To learn more about EPI2ME, visit https://nanoporetech.com/products/analyse/epi2me/ or sign-up for a free Seqera Cloud account now.