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Old 03-13-2013, 12:29 AM   #1
juckdnarocks
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Default Pacbio RS output

I happen to hear that one smrt cell can produce about 400M bases now, is that true? Could somebody provide some information ? We are making a schedule to sequence a plant.
Thanks for any insight.

Last edited by juckdnarocks; 03-13-2013 at 04:08 PM.
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Old 03-13-2013, 05:51 AM   #2
krobison
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That's quite a bit on the high side. A recent run yielded an average of 81Mb per SMRTcell

It may also depend on which chemistry you are running. XL/XL gives very long reads, but with a quality only apparently useful for scaffolding. XL/C2 gives higher quality.
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Old 03-16-2013, 06:49 PM   #3
juckdnarocks
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Quote:
Originally Posted by krobison View Post
That's quite a bit on the high side. A recent run yielded an average of 81Mb per SMRTcell

It may also depend on which chemistry you are running. XL/XL gives very long reads, but with a quality only apparently useful for scaffolding. XL/C2 gives higher quality.
Thanks krobison.
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Old 03-16-2013, 08:51 PM   #4
madbomber
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Quote:
Originally Posted by juckdnarocks View Post
Thanks krobison.
Also, keep in mind that the number krobison gave was what it is today. I think in a month that number doubles per the upcoming upgrade: http://blog.pacificbiosciences.com/2...echnology.html
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Old 03-16-2013, 09:55 PM   #5
ECO
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PacBio and the amazing people there never cease to amaze me...it will always be the most intense and rewarding place I've ever worked.

If you'll allow me to wax reminiscent...I started there when readlengths were 25bp at accuracies barely above the "monkey line". The long banner/poster above my cubicle on my first day terrified me...base-by-base progress towards the (then unthinkable!) 100bp read. About a year, later I personally collected (with several colleagues) the first 20kbp read on a prototype instrument.

This is the most tenacious company I could imagine, and their process and execution is second to none. 1GB of single molecule data per SMRTcell should be recognized as nothing but brutally hard work by the PacBio team. Every group from molecular biology*, hardware, software, enzymology, nucleotide/dye chemistry, has pushed every limit to get where they are today.

**my peeps.
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Old 03-17-2013, 09:35 AM   #6
scbaker
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Quote:
Originally Posted by juckdnarocks View Post
I happen to hear that one smrt cell can produce about 400M bases now, is that true? Could somebody provide some information ? We are making a schedule to sequence a plant.
Thanks for any insight.
After a nice conversation with PacBio CSO Jonas Korlach, I've updated the specs we maintain at BlueSEQ: http://blueseq.com/knowledgebank/seq...c-biosciences/

Runs can be optimized for throughput (two shorter runs for ~200Mb) or read length (one longer run for ~100Mb). Once the upgraded RS2 machine comes out, there will be no need for two runs per chip (as the scanner will be able to handle all 150k ZMWs at the same time). This will effectively double the "throughput" run to ~200-300Mb. PacBio has also announced plans to double that output again (by protecting the polymerase from photodamage), so by the end of the year they might have about 500Mb per run.
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Old 03-18-2013, 01:12 AM   #7
juckdnarocks
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Quote:
Originally Posted by scbaker View Post
After a nice conversation with PacBio CSO Jonas Korlach, I've updated the specs we maintain at BlueSEQ: http://blueseq.com/knowledgebank/seq...c-biosciences/

Runs can be optimized for throughput (two shorter runs for ~200Mb) or read length (one longer run for ~100Mb). Once the upgraded RS2 machine comes out, there will be no need for two runs per chip (as the scanner will be able to handle all 150k ZMWs at the same time). This will effectively double the "throughput" run to ~200-300Mb. PacBio has also announced plans to double that output again (by protecting the polymerase from photodamage), so by the end of the year they might have about 500Mb per run.
Thanks Shawn, the link is very informative.

Last edited by juckdnarocks; 03-18-2013 at 01:45 AM.
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