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Old 11-20-2011, 04:13 PM   #1
SOLiDance
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Default Parameters of PaciBio

Hi,everyone! Does anyone know anything about the Pacific Bio seq instrument work stats? I knew the error rate is about 15% one year ago.
I wonder has it been improved now? If i wanna control the error rate below 1~2%, what's the effective read length left now?
Thank you ! I'd appreciate if somebody who got one PacBio in lab share info.
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Old 11-21-2011, 05:01 AM   #2
GenoMax
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Error rate is still about the same. If you are running in the circular consensus mode (small inserts 300- 500 bp) then you are able to account for the error by depth of coverage.

While one can now get long reads (2 kb or more) you would need to deal with the error rate on your own if you have long inserts.
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Old 11-21-2011, 05:18 PM   #3
SOLiDance
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Thank for GenoMax , our lab is planning to do a denovo sequencing, Prof. wanna add some Pacbio data , but now I'm afraid it won't help us much~
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Old 11-22-2011, 04:31 AM   #4
GenoMax
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PacBio long reads will still be useful for hybrid assemblies. Specially if you are using something else to get read depth.
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Old 11-22-2011, 04:33 AM   #5
krobison
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You should also take a look through this presentation

http://schatzlab.cshl.edu/presentati...%20Meeting.pdf

while PacBio has a very high per base error rate, it may be a better approach for getting information across a few kilobases than alternatives such as mate pair libraries.
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Old 11-22-2011, 04:00 PM   #6
SOLiDance
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Thanks for the link!
But I still worry about how helpful it can be with such a high error rate~
Maybe 454 is better choice since the read length can be more than 500bp and hybrid assemble pipeline is more mature.
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