NanoOK Reporter

Introduction

NanoOK Reporter is a tool for real-time analysis of data generated by NanoOK RT. In the following text, we will guide you through analysis of data generated for the BAMBI project.

Please download NanoOK Reporter from https://github.com/richardmleggett/NanoOKReporter

Please download the BAMBI dataset from http://opendata.earlham.ac.uk/bambi/BAMBI_P8_2D_Local_070317.tar.gz

Running NanoOK Reporter

To clone from GitHub and run, type:

git clone https://github.com/richardmleggett/NanoOKReporter.git
cd NanoOKReporter
java -jar dist/NanoOKReporter.jar

Loading the BAMBI data

  • Untar the BAMBI dataset:

    tar -xvzf BAMBI_P8_2D_Local_070317.tar.gz

  • This is a NanoOK sample directory containing just the BLAST subdirectories - it is these that NanoOK Reporter uses.

  • With the tar file uncompressed, go back to NanoOK Reporter and click the “Choose…” button next to the “Sample directory” field and browse to find the BAMBI_P8_2D_Local_070317 sample directory that you just untarred.

  • Then select the ‘Template’ radio button and the ‘Pass’ radio button and click on “Load CARD” - this will load the CARD chunk data into NanoOK. You can follow it’s progress at the bottom of the window. When it has finished loading, click on the CARD tab in the set of tabs (“Stats/NT/Bacteria/CARD”).

  • You can move the slider to move back in time through the data.

  • You can click on “Load NT” to load the NT data. This will take slightly longer than for the CARD data.

Running with live sequencing

When running with live sequencing, you can force the latest data to be imported by clicking on “Load CARD” or “Load NT” again. This will not reload chunk files that have already been analysed.