Contents

01

Installation

02

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.

Installation

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

• wf-human-snp: a workflow for running small variant calling and annotation in human samples with Clair3. (Sample report) (Documentation)
• wf-human-sv: a workflow for the prediction and review of structural variants from whole human genome sequencing data. (Sample report) (Documentation)

Assembly

• wf-clone-validation: assembly of small plasmid sequences, for verifying the results of molecular cloning experiments. (Sample report) (Documentation)
• wf-bacterial-genomes: a workflow for running assembly or alignment of bacterial genomes and annotation. (Sample report) (Documentation)

Metagenomics

• wf-metagenomics includes the Kraken2 and Minimap2 software to facilitate the taxonomic classification of sequence reads from metagenome samples. (Sample report) (Documentation)

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.

Miscellaneous

• wf-artic: a Nextflow workflow for running the ARTIC SARS-CoV-2 workflow on multiplexed MinION, GridION, and PromethION runs. (Sample report) (Documentation)
• wf-mpx: a basic workflow for alignment of Monkeypox virus reads to a reference and alignment with flye. Produces a useful QC report.(Sample report) (Blog Post)
• wf-cas9: a workflow for analysing on-target, off-target, and background sequencing from a Cas9 native DNA enrichment experiment.(Sample report) (Documentation)