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EPI2ME Labs 22.08.01 Release

By Stephen Rudd
Published in Software Releases
August 24, 2022
2 min read
EPI2ME Labs 22.08.01 Release

Dear Nanopore Community

We are delighted to introduce two new bioinformatics workflows and a collection of updates and fixes to our EPI2ME Labs product.

New workflow, wf-single-cell for the analysis of single-cell transcriptomics data. This is based on the GitHub research tool, sockeye, developed by our Applications team. This new workflow provides usability through its pre-packaged Docker containers and EPI2ME Labs graphical user interface. The latest updates to Sockeye have been included. The sockeye software will be deprecated and we would recommend that issues are reported through this project’s GitHub. The workflow is currently available at version v0.1.0.

New workflow, wf-flu, for the analysis of FluA and FluB genomes prepared using the ligation protocol for whole flu genome sequencing - see protocol release note. This workflow prepares whole genome consensus sequences following FASTQ read mapping to the CDC multi-fasta Influenza reference. Strain typing is performed using the abricate software with an INSaFLU database. This experimental protocol is also based on work developed by our Applications team. More information can be found in a separate post.

Our workflow for transcriptome analysis, wf-transcriptomes, has been updated to include functionality for differential gene expression in addition to the previous reference and de novo based isoform detection and fusion gene detection functionality. The differential expression workflow uses the analysis logic from the EPI2ME Labs tutorial - the tutorial will now be deprecated in favour of the workflow. Please see the workflow’s CHANGELOG for additional information on fixes included in this release. The wf-transcriptomes workflow is tagged at version v0.1.5.

Our workflow for whole human genome variation analysis, wf-human-variation, has been updated to version v0.1.1. This update includes minor bug fixes and offers better control for alignment performance. Please see the CHANGELOG for further details.

wf-clone-validation, the workflow for assembling complete plasmids from rapidly sequenced plasmid preparations has been updated to version v0.2.4. This release includes a couple of minor fixes and the software now runs on computers installed with Windows/WSL. Please see the CHANGELOG for additional information.

The epi2melabs-notebook container image used by the EPI2ME Labs desktop application has been updated to version v1.1.34. This release includes the new wf-flu and wf-single-cell workflows. Please update your EPI2ME Labs installation with the “Environment update” button provided through the settings cog at the bottom left of your EPI2ME Labs panel.

Our workflow for whole human genome SNP analysis, wf-human-snp, is to be deprecated and will be removed from the EPI2ME Labs product in a future release. The SNP analysis software is now contained within the wf-human-variation software where it will continue to be developed and supported.

The EPI2ME Labs team would welcome recommendations for new workflows, tutorials, and functionality that you would like to see included in the product.


Tags

#notebooks#nextflow#workflows#releases
Stephen Rudd

Stephen Rudd

Bioinformatics product manager

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