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.

EPI2ME Labs workflows

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:

The wf-artic workflow can now report genotype information for the SARS CoV-2 spike protein’s genetic variants of concern
wf-alignment has been updated to include a demultiplexing step when processing barcoded sequence content
wf-hap-snps has improved reporting and a standardised report name
wf-demultiplex is a demonstration workflow that shows how Guppy demultiplexing may be included as a step in Nextflow pipelines

EPI2ME Labs components

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.

fastcat is a tool to identify and stream FASTQ-format sequences into downstream tools (e.g. alignment or de novo assembly) whilst harvesting basic sequence characteristics. This allows workflows to accommodate input sequences from creative directory structures and accommodates files that may be gzip compressed.
ncbitaxonomy is a lightweight tool featuring just the taxonomic classification functionality from the ETE3 toolkit. The ambition of this tool is the provision of functionality for assessing sequence collections in relation to overlaid information from the NCBI taxonomy database - this has applications in WIMP- and 16S-like workflows that address metagenomic classification such as wf-metagenomics.

Research software releases

Medaka v1.3.3

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.