EPI2ME Labs 22.11.01 Release

By Stephen Rudd
Published in Software Releases
November 16, 2022
1 min read
EPI2ME Labs 22.11.01 Release

Dear Nanopore Community,

With this month’s update to our EPI2ME Labs product we are delighted to introduce a new sequence basecalling workflow. We also include maintenance updates to several other workflows.

  • Our new workflow, wf-basecalling, uses a containerised Dorado installation to prepare aligned CRAM from FAST5/POD5 signal data. The workflow is released with tagged version v0.0.1 and additional information may be found from the product’s GitHub pages.

  • The wf-human-variation workflow now also includes Dorado as a bundled step for the basecalling of FAST5 (and POD5) format signal data. This replaces the earlier Guppy subworkflow. The update also includes a number of bug fixes and improvement to the documentation. Please see the project’s CHANGELOG for further information. This workflow is now tagged with version v0.4.0.

  • The wf-single-cell workflow now uses a modified transcript assignment method. The Salmon method for transcript mapping has been replaced with minimap2 - this change leads to the characterisation of additional gene transcripts. The update also includes a PCA preprocessing step prior to the UMAP transformation. Further information on these changes may be found in the CHANGELOG. The workflow is now tagged with version v0.1.5.

  • wf-metagenomics has been updated with bug fixes. The workflow is now tagged with version v2.0.2 and further information is described in the CHANGELOG.

  • The tagged v0.1.6 release of wf-transcriptomes includes both updates and fixes for the differential gene expression (DE) functionality. There are improvements to the DE documentation and an option to run DE analyses independently has been included. Please see the CHANGELOG for further information.

  • The deprecated workflows wf-human-snp and wf-human-sv have been removed from GitHub. Please use the wf-human-variation workflow instead.

  • We will be deprecating the option to run workflows using the conda profile

    • Users are advised to run our workflows using our container images via Docker [--profile standard] or Singularity instead [--profile singularity]




Stephen Rudd

Stephen Rudd

Director, Bioinformatics Product

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