Characterizing viruses using the PathSEQ Virome app in BaseSpace

The BaseSpace App store is continually expanding in the breadth and depth of applications, taking you from raw sequencing data through biological interpretation.  Today we’re happy to introduce a new App from PathGenDX called PathSeq Virome.

Whether you are looking for a contaminant in your biological sample, identifying an infection in your sample, or investigating new viruses, PathSEQ Virome can provide the answer. PathSEQ Virome is a BaseSpace app that automatically identifies and characterizes virus genomes from a sequencing run, in a comprehensive and systematic way. After streaming from MiSeq, NextSeq or HiSeq, sequencing data is filtered, matched against the PathSEQ virus database, and quality-controlled for false positives. Currently able to detect >50,000 clinically relevant virus genomes, the app outputs a PDF report from ~2GB of sequence data within an hour.  The report identifies the strength of the overall genomes matched, provides a confidence score to novel viruses (if related to any of the genomes in the database), while also identifying the genomic region of the match. If multiple viruses are present in the same sample, they are combined into the same report, with the highest matches first.

Getting started with PathSEQ Virome is simple. After running your sequence data on HiSeq or MiSeq,  click on “Apps” in the header in BaseSpace and select the PathSEQ Virome app.


Alternatively, you can also launch the app from a Project by clicking on the “Launch App” button and selecting PathSEQ Virome from the pull-down menu


Select your Project from the pull-down menu within BaseSpace, and PathSEQ will prompt you to select which samples in the project you want to analyze.  By default, the results will be saved to a new project folder named “PathSEQ_virome_results”.


Upon completion, BaseSpace will automatically send you the following email, if you have opted in for these notifications:


To get to the analysis report, simply click on the link in this email. All reports generated by the app are stored in a Project folder named “PathSEQ_virome_results”.  Clicking on that folder provides convenient access all the reports generated by the app.


Check out this demo dataset containing an example of results from the PathSEQ Virome app, it will be shared with your account once you click on that link. The PathSEQ Virome app is available for a free trial for all Sample data that is less than 500 MB in size and a paid version of the app will be available in the near future without that sample size limitation.

Didn’t find the viruses you were expecting? Contact PathGENDx to find out about their wet lab viral enrichment process to increase sensitivity.

We invite you to try it out.  PathSeq Virome comments and feedback are welcome through the PathGenDX portal:

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