Our May 2021 update to EPI2ME Labs brings a smörgåsbord of fixes, new functionality and a colourful new project website.
Jupyter3 upgrade and maintenance to the existing tutorials
The EPI2ME Labs software hosts the tutorials from a Jupyter server. With this month’s release, the EPI2ME Labs Docker containers have been updated to include the JupyterLab version 3.0.5 software. This upgrade from 2.2.9 brings a number of interface improvements and helps EPI2ME Labs deliver cutting-edge data science functionality. The existing tutorials have been updated to accommodate these changes and the IGV genome browsing tool that we maintain now works with this version of the Jupyter software.
Updates and maintenance to the wf-hap-snp, wf-artic and wf-alignment workflows
The EPI2ME Labs workflows have minor maintenance updates. The changes are largely aimed to the standardisation of the canonical workflow; we are aiming to use input FASTQ sequence data from a directory that may contain one or more files that may be compressed and/or barcoded. Other novel functionality in this release includes:
New tools and updates
The EPI2ME Labs and EPI2ME Labs workflows use a collection of actively-maintained packages that provide functionality for simplifying and abstracting common tasks. The aplanat Python package provides the toolkit for the preparation of graphs, charts and tables that are presented in our reports. Mapula is a Python package that provides observational insight from streamed mapping data (e.g. mapping quality and alignment identity). With this update we introduce two new tools to simplify sequence analysis in both tutorials and workflows.
Updated functionality for reporting reference (non-variant) alleles of interest in medaka variant Minor fix to medaka consensus; other changes and fixes are documented in the changelog.
We look forward to any feedback and would welcome ideas and insight for tutorials and workflows that would benefit your research.