New PacBio system: Sequel

[SNPsaurus]

http://blog.pacificbiosciences.com/2015/09/introducing-sequel-system-scalable.html

[AllSeq]

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.

[luc]

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).

[GenoMax]

Big if is would it work consistently. That has been our biggest gripe with RSII.

[Brian Bushnell]

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.

[GenoMax]

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.

[luc]

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) .

[Brian Bushnell]

It is possible that JGI has better control over samples/libraries. Do you only run internal samples?

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.

[SNPsaurus]

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.

[nucacidhunter]

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?

[ymc]

This box sounds exciting. Any words on reagent cost, accuracy and read length?

[AllSeq]

This box sounds exciting. Any words on reagent cost, accuracy and read length?

What 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.

[luc]

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.

[gringer]

What 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.

This is very close to the current cost of MinION sequencing. It wouldn't surprise me if that weren't a coincidence.

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.

[AllSeq]

I wonder how flexible PacBio are with their pricing for the chip and reagents.

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.