MiniSeq - a new addition?

[Jessica_L]

300 cycles and 16M reads (Illumina spec) for a MiSeq v2 kit is $1000. So, you're getting more MiniSeq reads but for a price increase that ends up keeping the cost per base about... yeah, the same. (~2E-5 cents per base if my napkin math is right)

And what JBKri said about error rates-- comparing to one of my last MiSeq runs, the error rates are about double. Is that typical for the 2-dye chemistry?

[jwfoley]

If we're comparing reads to reads, the more apt comparison is 150 cycles and 25M reads for a MiSeq v3 kit ($850). Does anyone know the pricing for the MiniSeq's 75-cycle kit?

[misterc]

$800 list for 75 cycles of "High Output" on MiniSeq. Catalog # FC-420-1001

[jwfoley]

Okay, so basically no cost-per-read advantage over the MiSeq either. I don't mind paying an extra $50 per run to double my read lengths. But if I were buying a new machine, that wouldn't be worth the extra $100k down payment plus the maintenance, so there's a place for it.

[Brian Bushnell]

Originally Posted by Jessica_L

And what JBKri said about error rates-- comparing to one of my last MiSeq runs, the error rates are about double. Is that typical for the 2-dye chemistry?

Double or more is typical in my tests of NextSeq, for example. But, the optics are different as well as the dye, so it's hard to say whether the 2-dye system causes it.

[jwfoley]

Originally Posted by Brian Bushnell

Double or more is typical in my tests of NextSeq, for example.

v2 chemistry or v1?

[Brian Bushnell]

V1 was around 5x or more the error rate of MiSeq, IIRC. V2 was closer to 2x. I only tested the very early V2 kits, though, though because it had major issues with bar-code calling for a long time, so we kept using V1.

[misterc]

2-channel imaging will always struggle to keep the intensities straight amongst the 3 lit bases in 2 images. Everything gets dimmer and less pure in signal as you go from cycle to cycle. This likely is what will drive higher error rates, as I doubt the SBS chemistry is to blame.

[Ingeneious]

Originally Posted by jwfoley

Okay, so basically no cost-per-read advantage over the MiSeq either.

There is a cost / read advantage if you are doing 2 x 150 PE sequencing. 50% of the capital cost of the MiSeq and the NextSeq-esque wash system also means less maintenance than the MiSeq.

Overally though, looks like it is targeted to researchers seeking to trade off the lower up front cost for slightly higher run costs and reduced capacity.

[M4TTN]

Info from Illumina:

The MiniSeq is similar to the technology utilised with our NextSeq platform based on 2-channel SBS chemistry.

Pricing Information

MiniSeq System (SY-420-1001): £35,653
MiniSeq Basic Plan (20004132): £3,350 for 1 additional year’s cover
MiniSeq Comprehensive Plan (20004133): £4,021 for 1 additional year’s cover

High Output Kit 	2 x 150 (300bp)	7.5	25	FC-420-1003	1,046
High Output Kit 	2 x 75 (150 bp)	3.75	25	FC-420-1002	652
High Output Kit 	1 x 75 (75 bp)	1.875	25	FC-420-1001	558
Mid  Output Kit	2 x 150 (300 bp)	2.4	8	FC-420-1004	384

So upfront and service costs are half a MiSeq.
Output for counting experiments is the same as MiSeq v3 chemistry (25 M reads)
The only thing it lacks are long paired reads 2x300 bp (but those kits are failing at the moment anyway...) and with NexteraXT many of our fragments are shorter than 300 bp anyway...

I think knowing what I know now...I'd probably buy one...specs are only going to improve.

[luc]

But counting applications are much better served by the HiSeq - if one does not need immediate turnaround.

Originally Posted by M4TTN

Info from Illumina:

The MiniSeq is similar to the technology utilised with our NextSeq platform based on 2-channel SBS chemistry.

Pricing Information

MiniSeq System (SY-420-1001): £35,653
MiniSeq Basic Plan (20004132): £3,350 for 1 additional year’s cover
MiniSeq Comprehensive Plan (20004133): £4,021 for 1 additional year’s cover

High Output Kit 	2 x 150 (300bp)	7.5	25	FC-420-1003	1,046
High Output Kit 	2 x 75 (150 bp)	3.75	25	FC-420-1002	652
High Output Kit 	1 x 75 (75 bp)	1.875	25	FC-420-1001	558
Mid  Output Kit	2 x 150 (300 bp)	2.4	8	FC-420-1004	384

So upfront and service costs are half a MiSeq.
Output for counting experiments is the same as MiSeq v3 chemistry (25 M reads)
The only thing it lacks are long paired reads 2x300 bp (but those kits are failing at the moment anyway...) and with NexteraXT many of our fragments are shorter than 300 bp anyway...

I think knowing what I know now...I'd probably buy one...specs are only going to improve.

[M4TTN]

Depends on how many reads you need...we are multiplexing 5-8 samples quite nicely on a MiSeq (counting expt). No need to go to higher depth for us (at least not at the moment).