Sequencing for enzyme discovery - Miseq or 454?

[rjoyons]

Hi everyone,

I'm very new to the world of next generation sequencing, I've been reading a lot about the different types and their advantages and disadvantages.

I want to construct a shotgun metagenomic library to find specific enzymes, but I have read that data from a Miseq is much more difficult to assemble due to the short reads it produces. Is this still true even with the new 250 bp setting?

my options are to use a Roche 454 GS FLX+ or a Miseq
I know 454 has been used to construct metagenomes successfully but I also know using a Miseq is much cheaper, so just looking for a bit of advice about which is best to use.

Thanks in advance!

[TonyBrooks]

We've moved from 454 to MiSeq for our metagenomes.
If you're careful with your library construction, then the MiSeq should be easily as good as the GS FLX. We tend to gel cut our libraries to have inserts around 400-450bp. We can then align paired reads together using something like Flash and treat them as we would 454 reads.
300bp reads should be coming soon (and possibly 400bp) so we can go for even longer.
I can't comment on GS FLX+ as we didn't get the upgrade.