IGV for EPI2ME workflows

By Bede Constantinides
Published in Articles
June 10, 2024
1 min read
IGV for EPI2ME workflows

While we strive to automate data analysis as much as possible, producing summaries, variant calls and sometimes full interpretations of sequencing data, it’s still very important to understand the raw data behind our results. It can be useful to poke and prod at the raw sequences underlying, for instance, a marginal variant call, or the arrangement of a structural variant. Sirisha recently wrote about doing this in her practical guide to reviewing BAM files. To further streamline the process of manually reviewing workflow outputs, we’ve added built-in support for the Integrative Genomics Viewer (IGV) in the latest version of the EPI2ME Desktop app.

We’re adding IGV to all of our workflows where read-level exploration is useful, starting with the five supported today. Whether for identifying PCR artifacts with wf-amplicon or quality controlling vector-based biopharmaceuticals with wf-aav-qc, IGV offers an interactive, read-level view of your sequencing data without leaving the EPI2ME app. As of version 5.1.14, IGV is available in the following workflows from the new Viewer tab:

  • wf-alignment: Are aligned reads of good quality; do they have secondary alignments?
  • wf-amplicon: Are there any unexpected variants, perhaps at low frequency?
  • wf-metagenomics & wf-16s: Is a taxonomic assignment supported by even read coverage?
  • wf-aav-qc: Are there any sequence changes or structural abnormalities in the product?

Scrutinising variant calls using IGV in EPI2ME Desktop

Using IGV working inside EPI2ME

Running the wf-amplicon workflow using built-in test data now generates a tab named Viewer. Opening this reveals an interactive IGV track showing read support for the reference sequence. Nucleotide positions differing from the reference sequence are displayed as coloured blocks. In this case we see well-supported nucleotide substitutions at reference positions 315 and 318.

This functionality is implemented by embedding a IGV.js instance in the Viewer tab of the EPI2ME app. As soon as an IGV config file is produced by a workflow and all of the files referenced within it are present, the Viewer tab automatically renders an IGV browser. Try it for yourself by downloading EPI2ME Desktop.




Bede Constantinides

Clinical bioinformatician

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Scrutinising variant calls using IGV in EPI2ME Desktop
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