EPI2ME 24.02-01 Release

By Stephen Rudd
Published in Software Releases
February 07, 2024
2 min read
EPI2ME 24.02-01 Release

Dear Nanopore Community,

We are delighted to release a magnificent collection of updates and improvements to our EPI2ME workflows. 

  • wf-clone-validation [v1.1.0] - introduces a new --large_construct parameter to enable the assembly of larger plasmids and Bacterial Artificial Chromosomes (50,000-300,000bps).
  • wf-pore-c [v1.1.0] 
    • The newly added --bed parameter will prepare a BED output file compatible with downstream tools including the Yahs scaffolder.
    • Introduces compute resource management improvements including a --max_monomers parameter to filter out reads which contain more than this number of monomers, see the Changelog for more details. 
  • wf-transcriptomes [v1.1.0]
    • Output improvements for differential gene expression analyses that include
      • adding a gene_name column to de_analysis count TSV files.
      • additional read count output files including gene count per million reads and unfiltered transcript counts mapped with gene names.
    • The workflow will now run to completion when no reference annotation is provided; the output transcriptome will however be unannotated.
    • The mapping processes are now multi-threaded.
    • Increased memory allocation for JAFFAL process to prevent out of memory errors.
    • Transcript summary tables are now also published into the output directory.
  • wf-aav-qc [v1.0.3] - Improvements include better datatype handling.
  • wf-single-cell [v1.0.3]
    • The transcriptome sequence and annotation files prepared during the run are now published into the output directory.
    • Improved datatype handling during the tagging of BAM files.  
  • wf-metagenomics [v2.9.0]wf-16S [v1.1.0]:
    • Swaps the plotting backend for the barplot in the report from eCharts to Bokeh.
    • Default for --n_taxa_barplot increased from 8 to 9.
    • The --database_set parameter is now Standard-8 when the --classifier parameter is set to kraken2.
    • Bug fix with custom databases in the kraken2 and real-time pipelines.
    • Updated memory resources.
    • The workflow now accepts BAM files (as produced by Dorado) as input.
  • wf-human-variation [v1.11.0] updates Straglr to fix some inconsistencies in the output VCF and appease VCF validator software. The latest version also ships with several performance improvements which will noticeably reduce workflow run time. 
  • wf-somatic-variation [v1.0.0] adds a tumor-only mode for the base workflow, better resource directives to improve workflow robustness and several quality-of-life fixes.
  • wf-bacterial-genomes [v1.1.0]
    • Workflow now uses Flye’s --nano-hq parameter for the de novo assembly. Additionally, Flye’s --genome-size and --asm-coverage parameters are available in the workflow as --flye_genome_size and --flye_asm_coverage, respectively.
    • Improved memory allocation.
    • A summary of results for all samples are now collected in JSON format in file results.json.
    • Bug fixes to generate reports when the de novo assembly fails.
  • wf-flu [v1.1.0]
    • Downsampling is now turned off by default.
    • Added a new parameter (--rbk) to improve downsampling of RBK data.
    • Bug fixes to generate reports when no samples undergo nextclade analysis. 
  • wf-alignment [v1.1.0]
    • Dropped limit of 20 for --thread parameter.
    • BAM tags in uBAM input files are now carried over to the output.
    • Fixed depth plots in report appearing mangled in some situations.
    • Now produces an MMI index file that can be re-used to reduce execution time when running the workflow again on the same reference.
    • --reference_mmi_file option to use a pre-generated MMI index file as reference.
  • wf-amplicon [v1.0.3]
    • Better handling of whitespace / special characters in input file names.

The EPI2ME desktop application is now available tagged at version v5.1.9. The latest release includes improvements to stability and installation and is available from the project downloads page.

  • The minimum allowed version of WSL required for workflow execution on Windows devices has been increased to 2.0.14. You should be prompted to update within the setup wizard, if your WSL version is not already up to date.
  • Login to the app is now available for early access users of our new EPI2ME cloud platform. We greatly welcome your feedback! There is more information on this upcoming product and release timelines are described in this earlier note.

We welcome any feedback and would love to hear your recommendations for future workflows, new features or additional functionality.




Stephen Rudd

Stephen Rudd

Director, Bioinformatics Product

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