EPI2ME 23.06-01 Release

By Stephen Rudd
Published in Software Releases
June 14, 2023
1 min read
EPI2ME 23.06-01 Release

Dear Nanopore Community,

With this first June release, we are delighted to update our EPI2ME workflows with some exciting new functionality and a number of other improvements.

  • wf-cas9 (v0.1.11) has been updated as a minor release that updates the default resource parameters.
  • wf-bacterial-genomes (v0.3.0) has been updated to include an --isolates mode. This introduces some exciting new functionality:
    • MLST characterisation has been added to the workflow to identify the species and sequence type from the genome assembly alone.
    •  The pointfinder method from Resfinder is run automatically using species information determined by the MLST analysis step described above. This update accommodates isolate samples of unknown species, or runs where you have multiple barcoded isolates, and will provide a full AMR analysis.
    • The HTML format report produced after an analysis has been revised with some dramatic new figures. Single sample reports are now also produced alongside the normal overall run report.
  • wf-human-variation (v1.6.0) is a minor release and solves an issue when calling CNV from CRAM format starting files.
    • The included wf-basecalling (v0.7.1) component has also been updated and includes other minor fixes. 
    • the --snp analysis will now produce VCF format output files that now also contain functional annotations from SnpEff. The HTML report now includes a table of variants annotated using the ClinVar resource.
  • wf-transcriptomes (v0.1.13) has been updated to provide a bug fix when the de novo transcriptome workflow path is run.
  • wf-pore-c (v0.0.8) has been updated to improve the workflow documentation and to provide a more comprehensive description of the output files and to update the help texts made available through the EPI2ME Labs desktop software. The existing chunk_size parameter has been updated to a default value of 25000 - this will address some memory usage issues.
  • wf-somatic-variation (v0.2.0) has been updated to include new functionality for the calling of somatic SV using nanomonsv. Several minor bugs have also been fixed and the documentation has been expanded.
  • wf-amplicon (v0.2.0) has been updated to also report observed low coverage variants in an additional table.
  • wf-single-cell (v0.2.5) has been updated to improve the handling of system resources - this resolves out of memory issues when processing larger datasets.

We would welcome recommendations for new workflows that would benefit your research and would love to hear about new functionality to our existing workflows.




Stephen Rudd

Stephen Rudd

Director, Bioinformatics Product

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