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Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com -
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. -
Seven times more data per SMRT-cell is promising.
Half the price of the RSII sequencer? "only" $350,000?
(... the RSII is much better looking than this fridge).Comment
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Big if is would it work consistently. That has been our biggest gripe with RSII.Comment
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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.Comment
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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.Comment
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We see quite a lot of clearly reagent-related variation (e.g. several batches of SMRT-cells did require loading with enormous library concentrations this summer) .Comment
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No... most of what we sequence comes from remote users. But, we do all the library construction here, and I believe we reject samples that do not have high molecular weight DNA, or insufficient mass.Originally posted by GenoMax View PostComment
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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.comComment
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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?Comment
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This box sounds exciting. Any words on reagent cost, accuracy and read length?Comment
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What they've said so far:Originally posted by ymc View Post
$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.Comment
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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.Comment
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This is very close to the current cost of MinION sequencing. It wouldn't surprise me if that weren't a coincidence.Originally posted by AllSeq View Post
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.Comment
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My guess (with no evidence to back it up) is that PacBio won't directly compete with the MinION until ONT demonstrates that it can achieve the same level of de novo consensus accuracy. Until then, PacBio will just focus on the high quality sequence they generate and 'let' ONT have the portable market. If ONT can match the data quality, then PacBio could be in real trouble.Originally posted by gringer View PostComment
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM
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