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Old 02-18-2012, 05:56 AM   #13
Geneus
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Location: New Jersey

Join Date: Dec 2010
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Quote:
Originally Posted by gringer View Post
If this is a raw per-molecule error (as I assume with a "single molecule" technology), then I consider it acceptable. Illumina and SOLiD technologies use hundreds of identical sequencing reactions per cluster to generate a consensus read, and it's unlikely they would have the same accuracy with single molecules per cluster.

It has been mentioned that the errors are almost entirely deletion errors. It would be possible to sequence more molecules and do a fairly simple alignment process on the sequences to identify deletions and get a consensus.

Assuming the error is random enough (bearing in mind the press releases suggest there is some bias), multiple sequencing experiments should increase the chance of a reliable read fairly quickly. With two strands sequenced (e.g. forward and reverse) and completely random error, you double the Q value (i.e. from ~Q14 / p = 0.04 to ~Q28 / p = 0.0016). The bias would increase the chance of two strands having an error at the same location, which would probably mean there'll be some tricky regions that still can't be sequenced accurately, regardless of how many times it is done in parallel.

Bear in mind that tricky regions are already accepted as a fact of life with previous sequencing technology. In particular, very long highly repetitive regions, or regions that are hypervariable within individuals are a problem with current technology.

Excellent synopsis...thank you.
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