Table of Contents

• Introduction
• Licensing and registration
• Running DISCOVAR de novo on Breezy

Introduction

DISCOVAR de novo is a whole-genome shotgun assembler targetting 250-base Illumina PCR-free fragment reads. (A companion program DISCOVAR, for variant calling and assembling small genomes has not been installed.)

License and registration

The software is free to use, but, you are encouraged to register.  License and registration details are on the download page at the DISCOVAR site.

Running DISCOVAR de novo on Breezy

The software has been installed in /global/software/discovar/discovardenovo_52488/bin, with the main executable being DiscovarDeNovo.  To run that program, set up your environment with a module command:

module load discovar/52488
DiscovarDeNovo NUM_THREADS=$PBS_NUM_PPN <other_arguments>

To see all the command line arguments, use the --help special argument:

DiscovarDeNovo --help special

There is very limited documentation in /global/software/discovar/discovardenovo_52488/share/doc/discovardenovo .