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Old 05-28-2012, 07:30 AM   #1
AFBrito
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Default What's the best assembler for 454 reads?

Hi,

I would like to know what is the best assembler for 454 reads (Free software, if possible)?
I'll sequence viral genomes and I have a reference genome to guide the assembly!

My research group uses MAC OS and Windows operating systems.

Best regards,

Brito
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Old 05-30-2012, 02:07 AM   #2
flxlex
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Try Celera (http://sourceforge.net/apps/mediawik...itle=Main_Page) which came out pretty good in this study.

Another one of the best 454 assemblers is newbler, to be obtained for free from Roche at http://454.com/contact-us/software-request.asp, but you will need a Linux system for that. Another linux alternative is MIRA (http://sourceforge.net/apps/mediawik...itle=Main_Page).
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Old 05-30-2012, 06:11 PM   #3
AFBrito
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Hi flxlex,

Firstly, thanks! I read that work. CABOG and Newbler seem to be the best options. I'll deal with genomic sequences with some repeated regions, and I think these assemblers probably will yield good results (I hope so!). I'll try them!

Best,

Brito
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Old 05-31-2012, 05:38 AM   #4
kga1978
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The Broad also recently released assembly and (common error) cleanup tools for 454 data - I have used them with great success.

http://www.broadinstitute.org/scient...lysis-software
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