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Old 07-11-2013, 03:48 AM   #2
TonyBrooks
Senior Member
 
Location: London

Join Date: Jun 2009
Posts: 298
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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.
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