AB takes a lot of flak for what is arguably a major strength of their methodology: dual base encoding. Yesterday someone mentioned to me that dual base encoding was only an advantage when one had a reference sequence to map to.
We haven't tried de novo assembly on SOLiD data sets much, so I did not really argue the point at the time. However, in retrospect, I do not see any reason that the benefits of dual base encoding would not play out in de novo assembly. That is, a single base miscall might be recognized as a miscall in the context of other reads assembling into the same contig.
But do color space aware de novo assemblers take advantage of dual base encoding? Anyone know?
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Phillip
We haven't tried de novo assembly on SOLiD data sets much, so I did not really argue the point at the time. However, in retrospect, I do not see any reason that the benefits of dual base encoding would not play out in de novo assembly. That is, a single base miscall might be recognized as a miscall in the context of other reads assembling into the same contig.
But do color space aware de novo assemblers take advantage of dual base encoding? Anyone know?
--
Phillip
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