EPI2ME 24.03-01 Release

By Stephen Rudd
Published in Software Releases
March 06, 2024
2 min read
EPI2ME 24.03-01 Release

Dear Nanopore Community,

We are delighted to release a mammoth collection of updates and improvements to our EPI2ME workflows. And a new dataset release to boot!

  • wf-bacterial genomes [v1.2.0]
    • NEW! Salmonella serotyping is automatically performed when Salmonella is detected with MLST analysis. This functionality is provided by the integration of SeqSero2 into the workflow.
    • Read length filtering of reads < 1kb is now performed by default. This can be adjusted using --min_read_length.
    • A new --client_fields parameter can be specified to add extra info to the report.
  • wf-human-variation [v2.0.0]
    • NEW! Version 2.0.0 introduces Spectre (https://github.com/fritzsedlazeck/Spectre) as the default CNV caller. Users can still use QDNASeq with the newly added “use_qdnaseq” option.
    • This update introduces performance improvements when CRAM is supplied as an input, and fixes a bug that prevented tandem repeat BED files from being selected in the EPI2ME Desktop Application.
  • wf-clone-validation [v1.2.0]
    • NEW! Option to change the assembly tool to Canu with --assembly_tool, flye still remains the default assembler.
    • The --client_fields parameter can be specified to add extra info to the report.
  • wf-single-cell [v1.1.0]
    • Adapters and barcodes are now trimmed from reads before their alignment to the reference genome.
    • Added an option --full_length_only (default true), to process only read segments with two flanking compatible adapters.
    • Fixed an issue where minimap2 was searching for splice sites on the incorrect strand for 3prime/multiome data.
  • wf-transcriptomes [v1.1.1]
    • Improved handling of different annotation file types (eg. .gtf/.gff/.gff3) in de_analysis mode and bug fix to accommodate 10 or more samples in de_analysis.
  • wf-artic [v1.1.0]
    • To facilitate the identification of the latest clades and lineages of SARS-CoV-2 we have updated Nextclade to V3.
  • wf-metagenomics [v2.9.1] / wf-16s [v1.1.1]
    • Update to accommodate long argument list lengths when using glob patterns.
    • Fix to address a Kraken2 pipeline issue where incorrect numbers for unclassified counts were reported.
  • wf-somatic-variation [v1.1.0]
    • Updated ClairS to v0.1.7.
    • Support for the latest ClairS Dorado models.
    • Performance improvements that should appreciably reduce the run time of the workflow.
  • wf-basecalling [v1.1.7]
    • Bug fixed where incremental reports were not produced during live basecalling with the watchPath functionality.

Our collection of bioinformatics howto articles has also been growing. If you are unfamiliar with the EPI2ME blogposts, recent articles include helpful guides on topics that include

  • The usage of IGV to review and explore BAM files - such BAM files are a fundamental output from several workflows that include e.g. wf-alignment, wf-human-variation and wf-metagenomics (when run using the minimap2-based classifier).
  • A quickstart guide on how to benchmark accuracy when assessing genetic variation. This article introduces some of the terms that are used and stresses the importance of appropriate truthsets.
  • How to for VCF format files that describe genetic variation. This article helps demystify this file format and helps with wrangling specific data facets.

Finally we have a updated data release for the COLO829/COL0829BL tumour/normal pair of cell lines. This dataset improves the single-molecule read accuracy and read length characteristics of our previous dataset and uses the new 5kHz sampling frequency in line with current default sequencing device setup. Download links and instructions are available on the data release page.

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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