EPI2ME 23.10-01 Release

By Matt Parker
Published in Software Releases
October 06, 2023
1 min read
EPI2ME 23.10-01 Release

Dear Nanopore Community,

We are delighted to release a collection of updates and improvements to our bioinformatics software collection.


The EPI2ME Desktop Application [v5.1.3] provides a GUI that simplifies the usage of our bioinformatics workflows. This software update introduces a collection of usability improvements.

  • Addition of HTTPS proxy support - further proxy support is planned for the future. Users may provide an HTTP or HTTPS proxy address to the application. An HTTP proxy should be used only when it supports redirecting HTTPS traffic via tunneling.

    Please note: users on MacOS and Linux operating systems will need to separately configure Docker’s proxy settings (via Docker Desktop on MacOS and on the Command Line on Linux) (Docker daemon)

  • Multiple fixes to support Windows users with spaces or special characters in their usernames.

  • Improved management of the download and installation of EPI2ME WSL distribution during setup; interrupted installations are now handled.

  • Updates to the “Report Issue” functionality on Windows computers.

  • Bioinformatics analyses will now be updated as ‘Stopped’ if they become stuck in ‘Running’ or ‘Unknown’ states - this may occur following unexpected shutdowns.


wf-metagenomics - v2.6.0 / wf-16s - v0.0.2

  • Fixed the plots perturbed by the presence of quote symbols in NCBI taxon names.

  • Added a new output; an abundance_table_<rank>.tsv is now reported for the last analysed taxonomic rank.

  • An optional --minimap2_by_reference parameter has been added; this will output additional information on the sequencing depth and coverage for mapped reference sequences.

wf-human-variation - v1.8.2

  • Performance improvements to the SNP subworkflow when using BED files to define genomic regions of interest.

  • Fixed an issue with the SV HTML report generation.

  • Improvements to the ClinVar-annotated VCF.

wf-somatic-variation - v0.5.0

  • Updates to include the annotation of SVs.

  • Clair v0.1.5 is now included in the supplied containers.

  • Other nonspecific improvements.

wf-transcriptomes - v0.4.1

  • Added support for LSK114 direct cDNA sequencing via a Pychopper update (see below).

wf-single-cell - v0.2.8

  • Increased memory allocation for adapter_scan to fix out-of-memory issues.

  • summarize_adapter_table updates to increase memory-efficiency.

  • Fixed bug that was causing single base read truncations.

pychopper - v2.7.9

  • Added support for data generated by the LSK114 direct cDNA sequencing kit.

We welcome all feedback and would appreciate any information on your experiences with the new proxy functionality that has been added to the Desktop Application.




Matt Parker

Matt Parker

Director, Clinical Bioinformatics Software

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