Differences in Consensus Sequences

bhan · 08-01-2011, 08:36 AM

Hello everyone,

I'm trying to automate some data collection, and I need a consensus sequence generator.

Thus far, I've been using Geneious's built in consensus sequence generator, which has worked well. The only issue is that it is not command line accessible.

I found that the samtools mpileup command shown at http://samtools.sourceforge.net/mpileup.shtml generates a consensus sequence of the same length as the Geneious consensus but is only ~93% identical.

What might be causing these differences? Does anyone else know of a good standalone consensus sequence generator?

Thanks

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08-01-2011, 08:36 AM	#1
bhan Junior Member Location: Cambridge, MA Join Date: Aug 2011 Posts: 3	Differences in Consensus Sequences Hello everyone, I'm trying to automate some data collection, and I need a consensus sequence generator. Thus far, I've been using Geneious's built in consensus sequence generator, which has worked well. The only issue is that it is not command line accessible. I found that the samtools mpileup command shown at http://samtools.sourceforge.net/mpileup.shtml generates a consensus sequence of the same length as the Geneious consensus but is only ~93% identical. What might be causing these differences? Does anyone else know of a good standalone consensus sequence generator? Thanks