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Old 11-02-2010, 08:09 AM   #1
volks
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Default Exact Call Chemistry -> Sequence space

the new 5500 series introduces an "Exact Call Chemistry" module, which brings higher accuracy and sequences in base space at the cost of longer run times:

Quote:
By adding an Exact Call Chemistry (ECC) proprietary probe to its market leading ligation chemistry, the company has demonstrated greater than 99.99% average single-read accuracy. This high-accuracy data is essential for the detection of minor variants in heterogeneous samples, a critical area of importance in cancer research. Further, the data is output in standard basepair format, allowing easier interface with third party tertiary data analysis tools.
link1 link2

anyone has info on how it works?
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Old 11-03-2010, 05:31 AM   #2
Kingpin31
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It runs a 6th primer that has a 4-base encoding scheme. The 6th primer provides base information so that the translation frame when going from color to bases is corrected even when a single color mismatch is introduced. The accuracy comes from the extra redundancy that is introduced with that 6th primer. Apparently, this 6th primer is an option when you need extra accuracy or performing applications that require all output In bases (e.g. De novo, metagenomics, etc).

Can't explain the math to save my life. It's all error correction codes, which are the same algorithms used in cell phones and communication networks. Look it up if you dare!
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Old 02-15-2011, 08:42 AM   #3
smarkel
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For details see SOLiD™ System accuracy with the Exact Call Chemistry module. Life Tech gave a webinar today on the new XSQ format, which includes support for ECC. Slides and supporting documentation will be posted at http://solidsoftwaretools.com/gf/project/xsq.
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Old 02-15-2011, 10:13 AM   #4
pmiguel
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Quote:
Originally Posted by Kingpin31 View Post
It runs a 6th primer that has a 4-base encoding scheme.
3 base encoding.

Primers 1-5, same as normal--dual base encoding. Primer 6, three base encoding. So I guess the expected run time would increase by 20%.

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Phillip
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