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Deprecation of several EPI2ME Labs tutorials

By Neil Horner
Published in Announcements
June 01, 2022
1 min read

In the coming weeks the EPI2ME Labs team will be rejigging our tutorial and workflow offerings to remove duplication and provide the best bioinformatics experience possible.

EPI2ME Labs provides ONT customer with two main offerings that help them get up to speed with long read data analysis:

  • Jupyterlab-based notebook tutorials, which are a great teaching tool for walking a user through concepts while at the same time allowing the analysis of small amounts of real data.
  • Nextflow workflows that can process large amounts of real world data as described here.

Over time, some of the tutorials have become a bit stale and now contain outdated methodology. Others have been identified as being more suited to being implemented as a workflow. These tutorials have been removed from EPI2ME Labs. Please let us know if you rely on any of these tutorials, and we can point you to relevant alternative resources.

The remaining tutorials can still be found here.

Deprecated tutorials

The following are being removed from EPI2ME Labs:

  • Structural Variant Calling - our wf-human-sv performs the same task in a more streamlined fashion
  • Human Variant Calling with Medaka - this tutorial used an now deprecated methodology, users should instead use the wf-human-snp workflow.
  • Benchmarking GM24385 Small Variant Calling - this short tutorial introduced the hap.py tool for benchmarking small variants. We feel the tutorial did not add much over the documentation of the tool and the tool is now an option in wf-human-snp.
  • Cas9 Targeted Sequencing Tutorial - please see wf-cas9
  • ERCC Workflow - see wf-alignemnt, which is able to compare expected to observed counts of spike-in controls.
  • Introduction to Pychopper - see the instructions for using Pychopper here, pychopper is a preprocessing tool used within our wf-isoforms workflow.
  • Isoform Tutorial - see wf-isoforms for a more fullsome and automated cDNA/RNA preprocessing and classification workflow.
  • Metagenomic classification tutorial - please see wf-metagenomics
  • Viral and Bacterial Variant Calling - please see the workflow wf-bacterial-genomes

We are always keen to here feedback from our users. Were you using this notebooks? What aspects of them were useful to you? Would you like to see them make a return. Get in touch through the contact page.


Neil Horner

Neil Horner

Bioinformatician

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