EPI2ME Labs 23.05-01 Release

By Stephen Rudd
Published in Software Releases
May 03, 2023
2 min read
EPI2ME Labs 23.05-01 Release

Dear Nanopore Community,

With our first release of May, we are delighted to introduce two new workflows. We are also updating a number of other workflows to fix issues and enable better functionality on computers with ARM processors.

wf-somatic-variation (v0.1.0) is our new workflow for the analysis of somatic variation from paired tumour/normal sequence data. This workflow processes a pair of tumour/normal BAM files, prepares quality statistics and identifies candidate SNVs and short Indels using the ClairS software. The workflow generates two reports showing:

  • The alignment QC for the paired BAM files, facilitating their comparison.
  • A summary and descriptions of the variants identified.
  • Variant allele frequency plot, mutation type counts. Future updates to the workflow will include other ClairS functionality such as site genotyping/hybrid calling. Additional subworkflows for the detection of other variant types will also be added.

wf-amplicon (v0.1.0). This workflow facilitates the analysis of reads generated from one or multiple amplicons. After some pre-processing (filtering, trimming, downsampling), reads are aligned to a reference (containing the expected sequence for each amplicon). Variant calling is also performed using Medaka. The workflow analyses demultiplexed data and has been designed to work with our Native Barcoding kits. The generated report presents for each sample:

  • A section illustrating the number and quality of the raw and pre-processed sequence reads.
  • Tables summarising the alignment and variant calling results.
  • Plots showing the coverage along the individual amplicons. We plan to expand the functionality of wf-amplicon to also cover tiled amplicons and use cases where no reference is available in future releases.

wf-single-cell (v0.2.3) is our workflow for the analysis of single cell transcriptomics data. This contains two changes:

  • Fixes a bug which causes incorrect barcode assignment and addresses an out of memory error in cases where a chromosome has no mapped sequence reads.
  • Sequence reads that map to intron-only regions are now assigned to genes and are included in the gene expression analysis. 

wf-metagenomics (v2.2.0) is a workflow for the analysis of metagenomic sequence data. The workflow has been updated to run natively on ARM devices, notably recent Apple M1 and M2 processors. The workflow should now be considerably faster when running on such devices. Other updates include:

  • Updates to the existing databases and add a new kraken2 database, PFP8.
  • Fixes file names when exporting tables.

wf-pore-c (v0.0.4) receives a small update to fix the handling of modified base information during the digest step and a fix to the Chromunity output handling.

Finally wf-clone-validation (v0.3.0), our plasmid assembly and annotation workflow has been amended to use Flye instead of Canu for the initial assembly step.

We would welcome any feedback - especially for our new amplicon and somatic variation workflows.




Stephen Rudd

Stephen Rudd

Director, Bioinformatics Product

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