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-   -   how to optimize viral genome assembly in WGS 7.0? (http://seqanswers.com/forums/showthread.php?t=22175)

rexxi 08-01-2012 08:16 AM

how to optimize viral genome assembly in WGS 7.0?
 
Hi all there,

I'm reviewing another assemblers to try to get a lower number of contigs, for this I'm trying to use Celera assembler, but it gives me a lot of contigs. I was searching for information to optimize it in 454 technologies (this technology was used in it) but there are not clear examples for mi situation. I would be really glad if somebody gives me a suggest.

Thanks,

Oscar

flxlex 08-02-2012 12:01 AM

Obviously, I would recommend newbler from 454. However, there is also a program from the Broad specifically designed for your taks:

Quote:

AV454 (AssembleViral454) is an assembler, based on the ARACHNE package, designed for small and non-repetitive genomes sequenced at high depth. It was specifically designed to assemble read data generated from a mixed population of viral genomes.
Found here.


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