SEQanswers

Go Back   SEQanswers > Applications Forums > Metagenomics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Haplotype discovery - 454 data Raj Bioinformatics 2 06-22-2012 03:03 PM
454 - Concatenation miRNA Discovery - Giorgio C Bioinformatics 0 05-04-2011 12:38 AM
HELP: some suggestions for SNP discovery in 454? linikujp Bioinformatics 1 04-07-2010 12:39 AM
SNPs discovery with 454 pfranchini General 0 03-01-2010 11:43 PM

Reply
 
Thread Tools
Old 07-11-2013, 02:34 AM   #1
rjoyons
Junior Member
 
Location: Manchester

Join Date: Jul 2013
Posts: 4
Lightbulb Sequencing for enzyme discovery - Miseq or 454?

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!
rjoyons is offline   Reply With Quote
Old 07-11-2013, 02:48 AM   #2
TonyBrooks
Senior Member
 
Location: London

Join Date: Jun 2009
Posts: 298
Default

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.
TonyBrooks is offline   Reply With Quote
Reply

Tags
454 assembly, miseq 250bp, new to next gen

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 07:49 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO