We are pleased to release a new infectious diseases workflow and a collection of
minor updates to our EPI2ME Labs product.
Release of a new workflow, wf-mpx, with initial version v0.0.1 for the basic
analysis of sequence data prepared from samples containing monkeypox virus. The
workflow is now available through the EPI2ME Labs application. An article
describing the workflow, and providing some recommendations for how the mapped
sequence data might best be considered, can be found in a separate
Monkeypox Analysis post.
The wf-artic software for analysis of SARS-CoV-2 sequence data has been updated
to v0.3.16. This update includes an updated primer scheme for the NEB VarSkip
V2b design. There is also a change that allows for the passing of additional
parameters to the Pangolin software component - further details may be found in
the project’s CHANGELOG.
Several of the tutorials included in EPI2ME Labs have
been deprecated. Tutorials are intended to introduce data analysis concepts but
the Jupyter notebook is not an ideal vehicle for the production analysis of
sequence data. For production analysis of Nanopore sequence data we recommend
only our Nextflow-based workflows - these are simpler to run, have richer
analysis reports and are more actively maintained and developed. A separate post
explains more about the rationale behind this decision and
lists the tutorials that have been deprecated.
The EPI2ME Labs file browser has
been updated and simplifies connecting your sequence data to a workflow. A
collection of minor fixes have also been included in the update. These changes
have been implemented in the epi2melabs-notebook v1.1.21 container.
Our wf-isoforms workflow (v0.1.3) has been updated to use the latest version of
pychopper (v2.7.0) that now supports the SQK-PCS111 kit. Please see the
CHANGELOG for additional information.
We welcome any feedback and would love to hear recommendations for workflow or