Lane-tracking and non-ABI sequencers

Dom Spinella dspinella at chugaibio.com
Thu Sep 11 10:12:02 EST 1997


> I don't agree with you, I am a user of the Vistra system and very happy
> with the base calling software. The study that was done on sequencing
> facilities (it is available on the WWW but I can't recall the address)
> shows that accuracy is not linked with a brand, as the very same automatic
> sequencer could be in the top 10 as well as beeing ranked very low.
> What seems more important in the accuracy of the sequences seams to be
> the length of the migration.
 
Well I'm glad to hear that you have had good experience with your Vistra
system.  I have never used one, so I can't compare it to ABI.  However,
in my experience, the most important issue is the quality of the
template to be sequenced.  Almost any instrument will do a reasonable
job on ultra-pure single-stranded M13, but many fall down when it comes
to difficult or dirty templates.

> 36 lanes divided by 2 makes 18, I don't know how long take a run to
> complete on a ABI, but with a well trained technician one can makes 22
> samples per day on a vistra. 

Actually, the XL upgrade to the ABIs allows the simultaneous run of 64
lanes. Loading every other lane still gives us 32, which is quite a bit
ahead of your Vistra.  And of course if we manually track lanes, we can
use all 64 lanes. If we really push we can get two runs of each
instrument in per day.  Back when ABI was using 24 lanes, they too had
no tracking problems.  Its only when they tried to crowd more lanes into
the same width of gel that the tracking problems emerged.


> I am not affiliated to Vistra, but in my opinion, it is a good sequencer for > small sequencing program, very easy to use. 


I think you have hit an important point.  We run a medium-sized core
facility dealing with hundreds of templates per week.  In that scenario,
throughput is everything and here, for better or worse, ABI is the only
game in town.


> I don't have any problem of lane tracking (except when the sequence is very very bad) no blue blob or red thingy. I don't have to spend half an hour washing the plate because there is building up (I just use Decon, a classic detergent, rinse with ddwater and ethanol before pouring the gel) and, at least in Europe, the assistance is very friendly and most of the time efficient. There are problems, the worst beeing, it is very hard to do more than 22 samples per day, the plates beeing small, it is hard to read more
> than 700 bp
 

We clean ABI plates the same way with no problems.  700 bp is a fairly
typical length of read on an average double-stranded template.

>and there is no dye termination kit at the minute.

And I don't know that there ever will be until the ABI patents expire.
So once again for each template, you have to perform 4 reactions to our
one -- no problem unless throughput is a critical issue -- and for many
of us, it is.
> 
> I hope this will help you.



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