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Old 07-02-2014, 05:54 AM   #1
vanillasky
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Default Analyzing metagenomic contigs

I have just finished running an assembly with Metavelvet and now have the contig file. Since I am new to the assembly process I wanted to ask what programs can be used next to analyze these contigs?
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Old 07-02-2014, 07:20 AM   #2
cliffbeall
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MG-RAST or IMG-MER, maybe?

That's assuming you want to do annotation and you don't mind web-based tools.

Last edited by cliffbeall; 07-02-2014 at 07:21 AM. Reason: clarity
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Old 07-03-2014, 01:13 AM   #3
vanillasky
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What other options are there besides the web based tools? Are the stand alone programs more advantageous?
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Old 07-03-2014, 08:35 AM   #4
Brian Bushnell
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What do you want to analyze about them? I like Quast, which is not web-based.
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