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Old 08-01-2012, 07:16 AM   #1
Location: Santiago, Chile

Join Date: Jun 2012
Posts: 20
Question 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.


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Old 08-01-2012, 11:01 PM   #2
Location: Oslo, Norway

Join Date: Nov 2008
Posts: 415

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

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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