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New PacBio system: Sequel
Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.comTags: None
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It isn't exactly the 'desktop' system we were waiting for, but it looks like they made some pretty big improvements in a number of areas. I'd be a little bummed if I had just bought an RSII.
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We have 3 RSII's, and have not had any particular problems with their reliability. Perhaps you got a lemon?
For our uses, this is pretty revolutionary - we could replace our 3 RSII's with one of these (they take up lot of space) and double our throughput while drastically reducing the per-base cost.
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It does feel like we have a lemon.
It is possible that JGI has better control over samples/libraries. Do you only run internal samples? Being a core facility we get stuff all over the place and it has been impossible to get consistent P1 productivity. PacBio seems to have very narrow tolerances (compared to Illumina) on what makes a library good/productive.
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Originally posted by GenoMax View PostIt is possible that JGI has better control over samples/libraries. Do you only run internal samples?
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For de novo work especially this is very appealing. For a small facility though I would worry that a large investment could be nullified by MinION/PromethION. That's always true of any technology, but the risks seem higher here.Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com
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PacBio is an innovative company and in recent years they have released new chemistry almost every year which has increased sequencing yield and length. I can’t say that about Oxford Nanopore and in fact they have been very slow to develop a product that works. With current pricing they are the most expensive platform for Gb of data. Their celebrity style marketing and promotion also suggests that they may not have much to offer in near future and they are just trying to stall competition. With recent trends that even companies obsolete their own systems after a year why should one wait for ONT?
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Originally posted by ymc View PostThis box sounds exciting. Any words on reagent cost, accuracy and read length?
$700/chip (including sequencing reagents) for ~7Gb of output (5-10Gb)
Read length at launch will be 8-12kb (and then increase over time).
I'm not sure if they said anything about accuracy.
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They said the chemistry is identical to the RSII - basically it is a bigger SMRT-cell and optimized camera and computing at the moment. Other than the read numbers the specs are likely unchanged.
For bacterial sequencing the RSII might be preferable under some circumstances, since it already generates surplus data and running a SMRT-cell on the Sequel will likely cost twice as much.
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Originally posted by AllSeq View PostWhat they've said so far:
$700/chip (including sequencing reagents) for ~7Gb of output (5-10Gb)
Read length at launch will be 8-12kb (and then increase over time).
I'm not sure if they said anything about accuracy.
A great MinION run will currently put out about 1Gbp of sequence, but that will change substantially after fast mode kicks in (about 20x sequencing speed). I wonder how flexible PacBio are with their pricing for the chip and reagents.
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Originally posted by gringer View PostI wonder how flexible PacBio are with their pricing for the chip and reagents.
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