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-human-variation: our all-in-one human variation workflow consolidates the small variant calling from the previous wf-human-snp, structural variant calling from wf-human-sv, CNV calling from wf-cnv (all of which are now deprecated), as well as performing STR expansion genotyping. This pipeline performs the steps of the four pipelines simultaneously and the results are generated and output in the same way as they would have been had the pipelines been run separately. (Sample small variant report)(Sample structural variant report)(Sample CNV report)(Sample STR report)(Sample alignment report)(Documentation)
• wf-somatic-variation: our workflow for the analysis of somatic variation from paired tumour/normal sequence data. It processes a pair of tumour/normal BAM files, prepares quality statistics, identifies candidate SNVs and short indels using ClairS, structural variants using nanomonSV and modified sites with modkit. (Sample SNV report) (Sample SV report) (Sample mod report) (Sample read QC report) (Documentation)
• wf-trio: our workflow for analysing variation using trio human genomic data. The workflow currently performs small variant calling, small variant merging, joint genotyping, structural variant calling, structural variant merging and pedigree phasing.(Sample small variant report)(Sample structural variant 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)
• 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

• wf-flu Influenza A&B typing and analysis from Nanopore data. (Sample report) (Documentation)

Targeted Sequencing

• wf-amplicon: analysis of reads generated from PCR amplicons. After some pre-processing, reads are either aligned to a reference (containing the expected sequence for each amplicon) for variant calling or the amplicon’s consensus sequence is generated de novo. (Sample variant calling report) (Sample de novo consensus report) (Documentation)

Miscellaneous

• wf-teloseq: provides telomere length estimates from data generated with the Telo-Seq protocol.(Sample report) (Documentation)
• wf-pore-c: a workflow for converting data generated with the Pore-C protocol to outputs in a variety of standard file formats used by downstream tools. (Sample report) (Documentation)
• wf-aav-qc: a quality control workflow for recombinant andeno-associated virus (AAV) viral vector production. (Sample report) (Documentation)

Deprecated Workflows

The workflows below are deprecated and are no longer actively maintained or supported. They remain listed here to help users find legacy documentation. Where available, use the recommended replacement workflow.

• 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) (Documentation) (Blog Post)
• wf-tb-amr Mycobacterium tuberculosis workflow for multiplexed Nanopore sequencing data. (Sample report) (Documentation)
• wf-cas9: a workflow for analysing on-target, off-target, and background sequencing from a Cas9 native DNA enrichment experiment.(Sample report) (Documentation)