DISCOVAR performance tips

Are you getting the most out of your hardware when running DISCOVAR?
Take a look at our Computational Performance tips – they could help you get more bang for your computational buck!

DISCOVAR is a heavily multithreaded and memory intensive tool that will push your machines hard. Configuring your hardware to get the best performance isn’t straightforward, but with the right settings you may see significant improvements. After much experimentation and investigation, and with help from fellow DISCOVAR users, we have prepared a set of tips. We’ll continue to add and update them as we learn more, and we would like to hear about your experiences via our forum.

Cleaner assemblies

Revision 46631 contains a number of algorithmic improvements. In particular there are now less ‘false’ bubbles in assemblies.  These arise particularly in assemblies at high (> 60x) coverage, as one might have e.g. for a bacterium.  These bubbles have substantial support on both branches but examination of the quality score distributions of the read bases associated with both allows DISCOVAR to kill off one branch.