how to optimize viral genome assembly in WGS 7.0?

rexxi · 08-01-2012, 08:16 AM

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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08-01-2012, 08:16 AM	#1
rexxi Member Location: Santiago, Chile Join Date: Jun 2012 Posts: 20	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