EPI2ME Workflows

September 01, 2020
3 min read
EPI2ME 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 Quick Start page for a walkthrough of using our workflows through EPI2ME Labs. 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-basecalling provides Oxford Nanopore Technolgies Technologies’ signal processing and primary data analysis in the form of a Nextflow workflows. (Documentation)
  • 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)

Human genetics



  • wf-metagenomics includes the Kraken2 and Minimap2 software to facilitate the taxonomic classification of sequence reads from metagenome samples. (Sample report) (Documentation)
  • wf-16s classifies 16S/18S/ITS amplicons from your samples. A selection of databases are available for use including ncbi_16s_18s, ncbi_16s_18s_28s_ITS, and SILVA_138_1. (Sample report) (Documentation)

Direct RNA sequencing and cDNA

  • wf-transcriptomes: transcript assembly from cDNA or direct RNA reads using either a reference-guided or an experimental de novo reconstruction options. This workflow also provides differential gene expression and differential transcript usage analysis.(Sample report)(Documentation)
  • wf-single-cell is a research pipeline designed to identify the cell barcode and UMI sequences present in nanopore sequencing reads generated from single-cell gene expression libraries. (Sample report) (Documentation)

Infectious Disease

Targeted Sequencing



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