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.

 
