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Old 06-19-2009, 02:20 AM   #2
dan
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Location: Cambridge, England

Join Date: Jul 2008
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I'd like to know the answer to the exact same question. Anyone got any benchmarks for mapping 454 data? References?


Am I right in thinking that only the GS Reference Mapper uses the correct error model for the 454 data? Does anyone know how they actually do that? i.e. How is the alignment done in flowspace?

Actually, from the manual: "read to reference alignments are made in nucleotide space, the consensus basecalling and quality value determination for contigs are performed in flowspace."

So the questions are:

How is the consensus sequence created?
(How) could the mapping be improved by using flowspace, and does any software do that?
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