Question: What Tool Should I Use To Assemble Data Produced By A 454 Sequencer?
4
gravatar for Cupton
9.2 years ago by
Cupton40
Victoria, BC, Canada
Cupton40 wrote:

What do you like for assembling paired-end #454 sequence data? (for 200kb assemblies)

assembly open next-gen sequencing • 4.2k views
ADD COMMENTlink modified 8.5 years ago by Ketil3.9k • written 9.2 years ago by Cupton40
4
gravatar for Bioch'Ti
9.2 years ago by
Bioch'Ti1000
France (Avignon)
Bioch'Ti1000 wrote:

Hi Cupton,

Regarding the adjustment of the question, I would strongly advise you to read this webpage that summarize all the available (free and commercial) tools to assemble 454 data:

http://seqanswers.com/forums/showthread.php?t=43

Regards.

"Previous answer" below:

Anyway, if you are looking for an open source 454 assembler, I think that MIRA3 is the best candidate! It is running under Linux/OsX

Check: http://www.chevreux.org/projects_mira.html

Otherwise, you can have a look to Galaxy, an interesting emerging online tool: http://main.g2.bx.psu.edu/

Regards.

ADD COMMENTlink modified 9.2 years ago • written 9.2 years ago by Bioch'Ti1000
1

Can you do (de novo) assembly using Galaxy? Can't seem to find it...

ADD REPLYlink written 8.4 years ago by lexnederbragt1.2k

Galaxy is not really a tool but a collection of tools, most of which are unrelated to assembly. You should specify what tool in Galaxy do you have in mind.

ADD REPLYlink written 9.2 years ago by Istvan Albert ♦♦ 80k
3
gravatar for Ketil
8.4 years ago by
Ketil3.9k
Germany
Ketil3.9k wrote:

Generally, I'd use Newbler, which isn't open source, but comes with the 454 equipment. Some people claim Celera gives higher quality, but so far, results have been ambigous. I'd be wary of the de Bruijn-based ones, where I have seen very mixed results.

I'd also try to verify the assembly in any way you can, mapping reads (preferably idependent ones) back, mapping ESTs or BAC ends, etc, not just relying on statistics like n50.

ADD COMMENTlink written 8.4 years ago by Ketil3.9k
1

Highly agree! You will have to compare and verify different assemblies. and when it comes to open-source I don't think I want to see Newbler's source code (I had a look once a while ago)

ADD REPLYlink written 8.4 years ago by Michael Dondrup46k
1
gravatar for Ketil
8.2 years ago by
Ketil3.9k
Germany
Ketil3.9k wrote:

An interesting resource on this is Nick Loman's blog entry on assembling Ion Torrent data

http://pathogenomics.bham.ac.uk/blog/2011/05/first-look-at-ion-torrent-data-de-novo-assembly/

While not quite 454, the technology is similar in many respects.

Anyway, we got better results from Celera (approximately Newbler quality) than from CLC for 454 data, but your mileage may vary.

ADD COMMENTlink modified 10 months ago by RamRS22k • written 8.2 years ago by Ketil3.9k
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