EPI2ME 25.05-01 Release

With our London Calling 2025 EPI2ME release we are delighted to introduce a collection of improvements to our desktop application. We also introduce two entirely new workflows for (1) the analysis of genetic variation amongst human trios and for (2) the measurement of telomere lengths (see Protocol and Know-how for full details). The release also includes updates to a number of our workflows. We also introduce a couple of fabulous datasets that demonstrate the value of Nanopore long read sequencing in metagenomics and telomeric sequencing.

EPI2ME Desktop Application v5.2.5 provides a number of performance and stability improvements

• Improved stability when running community developed workflows in the app
• Enables cancellation of cloud analyses during the data upload stage
• Fixes an issue with the EPI2ME blog feed not loading on the app home page
• Fixes an issue with the reporting of EPI2ME cloud connection status
• Resolves a cloud instance status issue where failed uploads became stuck at the “Created” stage
• Addresses an issue with providing fractional values in workflow parameters
• User authentication for usage of the app is now a requirement - logging in to the application uses Nanopore Community credentials.

The EPI2ME Desktop application can be downloaded from the EPI2ME downloads page.

• wf-trio v0.9.0 is a new workflow for the analysis of combined whole genome sequencing data from a proband and both parents. This first release is focused on the calling of small variants, structural variants, and phasing of variants for the discovery and characterisation of proband variants. The discrete analytical steps in the workflow include
  • Small variant calling
  • Small variant merging and joint genotyping
  • Structural variant calling
  • Structural variant merging
  • Pedigree phasing
• wf-human-variation v2.7.0 is our workflow for the analysis of different types of human genetic variation.
  • Workflow now additionally uses INDEL information for variant phasing - please see Sean’s blog post at Phasing of small insertions and deletions
  • Update to Sniffles 2.6.2 brings much better performance for calling of larger structural variants - Philipp explains the improvements that should be seen in a blog post at Structural variant calling in wf-human-variation 2.7.0
  • A register your interest page has been created for a new human variation cloud offering.
• wf-teloseq v1.0.0 is a new workflow designed to analyse the DNA sequence output of the Telo-Seq protocol. The initial release of this workflow is focused on a speedy analysis of telomeric lengths, either using a sample matched reference to measure telomere lengths per chromosome arm, or, if such a reference is not available, providing a per sample length profile for all input sequences which were identified as telomeric. This workflow:
  • Applies discrete quality control filtering to each read, to only base telomere lengths on the most reliable reads
  • Assigns a telomere boundary to each read where it can be detected, but only creates reportable statistics from reads which pass all filtering.
  • Outputs a tagged BAM, tagging each record with the calculated telomere length and a quality control status. If a reference is not provided, the BAM is unaligned, otherwise the records in the BAM are aligned to the reference. This BAM can be used for further analysis and investigation.
  • Finally, a comprehensive telomere length analysis report is generated, providing detailed insights into the telomeric profiles of each sample.
• wf-single-cell v3.2.0 is our bioinformatics workflow for analysis of single cell transcriptomic sequence data.
  • This version update includes new functionality for fusion gene detection using ctat-LR-fusion.
• wf-somatic-variation v1.5.0 has been updated to enable tumour only structural variant calling. With this update, the workflow can be run in its entirety with paired tumour and normal samples or with just the tumour sample.
• The EPI2ME website dataset index page has been updated and now includes a tabular list of available datasets. With this release we introduce two new datasets from the Oxford Nanopore team - a Zymo fecal dataset and a Teloseq dataset that accompanies the wf-teloseq workflow product.

Four of our EPI2ME bioinformatics workflows are deprecated with this release. A workflow deprecation means that the affected workflows will no longer be maintained. Updates elsewhere within the EPI2ME workflow ecosystem will not be applied to these workflows and improvements to any of the bioinformatics software used in the workflow will not be migrated across. The software repository for these workflows are now archived and bug reports and feature requests cannot be communicated through GitHub.