Geneious: can I save fewer contigs for PE?

[HereBeDragons]

Hi all,

Im working with illumina paired end output. I used genomic DNA but am only interested in the assembly of the organellar genomes (relying on higher copy number to give sufficient sequencing depth and coverage)...so the assembly of nuclear reads into contigs is just clutter.
Using Genieous 5.4 I am getting millions of contigs. I was wondering if there is a way to save just the largest contigs (hopefully organellar) after the initial assembly steps? At the 60% point my assembly is slowing to a glacial crawl as it implements the paired end data. I need a way to speed things up.

Im completely new to this, any advice would be great!

[anli]

You can save the contigs. But there is a upper limit to how many.

If you are interested in only the organellar genomes why not try to randomly down-sample your dataset. The organellar genomes should be at much higher coverage, so it might help.