Hi Tyler, 

I am not quite sure if you need PacBio for linking the contigs. You might be better off with "mate-pair" (jumping)  library(s) of different sizes (5, 10, 15kb) that can help your bioinformatics for linking the contigs. 

Of course you may use PBio with broader range and less than 5ug. As customer you may request that, providing that you will not get any warranties from the facility that will do it.

just my2c

Hi Petre, 

Thanks for your input. We had considered generating some mate-pair libraries, but still with the large insert-sizes we will need a lot of input DNA. And with the cost of PacBio coming down, the thought was that we might as well have full-length sequences rather than paired short reads. Since the project has the funding to accommodate the increased cost. 

I have done illumina mate-pair with less than 1 ug. Your complexity is 1/15 of human genome so you should be OK with less DNA. Anyhow, I think that if you are missing some DNA fragments it is for a reason.... so PBio might help, however  I am not sure if it will give you all the needed information. Do you expect too many (long) repeats? 

Good Luck

No, actually the genome is of an internal parasite and is expected (based on related genomes) to have reduced repeat composition- something in the range of 20%. 

Thanks for the info. Our sequencing core facility also recommended we avoid using REPLI-g.