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Overview

Tablet is a lightweight, high-performance graphical viewer for next generation sequence assemblies and alignments.  The Tablet viewer supports the ACE, AFG, MAQ, SOAP2, SAM, BAM, FASTA, FASTQ, and GFF file formats.  Running Tablet requires an X-Windows session connection to the HPCC.  Remote off-campus connections for Tablet are likely to be too slow in most cases to be practical, and as such, on-campus Tablet X-Windows connections are strongly recommended.

Running Tablet

To load the Tablet module:

 

module load Tablet

 

Then simply launch the application with:

 

tablet &

 

On first startup, Tablet will create a dot-subdirectory in your home directory space called:

 

.scri-bioinf

 

This subdirectory contains user-specific configuration information.

The HPCC build of Tablet is currently configured with 2.5GB of RAM maximum.  Because Tablet is a high-performance viewer, it is strongly recommended that you run it on the dev-amd09 node for optimal results.

Temporary Files

Tablet generates a series of large temporary files containing assembly information.  The application defaults to using the "/tmp" space for these files.  It is recommended that you alter this setting to a high speed, high capacity disk location such as your scratch space.  To set your temporary file location:

  1. Click the red "ball" in the upper left hand corner of the screen
  2. Click on the "Tablet Options" button at the bottom of the pop-up window
  3. Select the "General" tab
  4. Set the temporary file location under "Cache Options"

The location set in this screen should be recorded in your ".scri-bioinf" directory, so setting it on launch each time should not be necessary unless you desire to make a change.