Epicentre vs Lucigen fosmid kits

[zizzlestick]

We are planning to create fosmid libraries of our genome of interest to help in the assembly. This is because the preliminary data we've generated show that up to 80% of the sequence is repetitive.

Has anyone here ever used the Epicentre CopyControl fosmid library production kit or the Lucigen CopyRight fosmid cloning kit or (still Lucigen) the NxSeq 40kb mate-pair cloning kit? Thoughts on which among them's better?

Our genome size is more than 2 Gb.

[nucacidhunter]

For a genome with 80% repetitive content, mate pair of any kind may not help assembly as they only sample junction sequence tags. With high repetitive genome those tags would map to multiple locations rendering them less useful. To overcome this issue one has to be very stringent with mapped distances which will result in low rate of informative mates. This effect along with low yield of unique mate pair tags from Fosmid clones will make this approach less successful. PacBio's recently released P6-C4 chemistry with long reads (10-15 kb) which yields 0.5-1 Gb/SMRT cell seems to be more cost effective approach which could result in better assembly.