EPI2ME Labs Workflows
September 01, 2020
2 min
EPI2ME Labs Workflows
Available workflows

EPI2ME Labs maintains a collection of Nextflow bioinformatics workflows tailored to Oxford Nanopore Technologies long-read sequencing data. They are curated and actively maintained by experts in long-read sequence analysis.

We are excited to offer our bioinformatics solutions using the Nextflow reactive workflow framework. Nextflow has been selected as a preferred framework because of its integration with container technologies, software package managers and its scalability to cluster- and cloud-scale installations. Nextflow also has growing user adoption through projects such as nf-core. These advantages will help us deliver varied workflows with minimal requirements for the installation of additional software.


See the Installation page for a walkthrough to guide installation of the pre-requisites for using our workflows through EPI2ME Labs.

For more information on running workflows through the EPI2ME Labs application see the Running a Workflow section of our quick-start guide.

Our workflows are also freely available to use from the command-line on Linux, macOS, and Windows through WSL2. See our Workflow Command-line Usage page for more information.

Available workflows

Below you will find a complete list of available workflows with a short description of each. Each description is accompanied by a link to the Github repository hosting the workflow and a sample workflow report.

Basic Tasks

  • wf-alignment packages the minimap2 software and streamlines the process of mapping sequence reads to a reference genome and preparing summary statistics. It can also analyse the abundance of known molarity control experiments and use this information to derive the abundances of other species present in the sample. (Sample report) (Documentation)
  • wf-demultiplex packages the standard Oxford Nanopore Technologies read demultiplexing software. Other workflows include this step such that this workflow is not typically required to be run in isolation; it is supplied however supplied standalone for users that require it. (Sample report)

Variant Calling



Direct RNA sequencing and cDNA

  • wf-transcript-target to review and consolidates transcripts of interest from direct RNA sequencing collections. This workflow can also be used for more general assessment of transcripts of interest. (Sample report) (Documentation)
  • wf-isoforms: assembly and annotation of transcripts from cDNA or direct RNA reads. This pipeline provides both reference transcriptome-guided consensus and an experimental de novo reconstruction option.


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