[Bioc-sig-seq] Illumina vs. ABI Solid

Sulev Kõks Sulev.Koks at ut.ee
Wed Dec 23 08:16:22 CET 2009

It actually depends... I'm not so convinced on the superiority of  
Illumina. In fact, I know labs where Illuminas collecting dust.

We use SOLID 3plus and are very satisfied. One very important issue  
for us - SOLID is the ONLY platform what allows to preserve  
strandedness. For any kind of RNA seq applications, this is actually  
cornerstone for the analysis of transcriptome. Without this  
information you just throw away substantial part of the data.

There is no price difference between platforms - but with one run in  
SOLID you get up to 60 GB of reads. Illumina doesn't reach this yet.

So, I do not think that Illumina is better than SOLID. There are labs  
who prefer Illumina, and labs who prefer SOLID. SOLID came out later  
and lost a lot of market share, but this is not the reason to think  
its worse that Illu.


On 23.12.2009, at 4:02, Steve Lianoglou wrote:

> Hi,
> 2009/12/22 Droit Arnaud <Arnaud.Droit at ircm.qc.ca>:
>> Hi all,
>> The institute where I currently work is in the process of buying a  
>> new HT sequencer. We are debating whether we should get an Illumina  
>> or a Solid sequencer. I was wondering if anyone of you could give  
>> me some advice in terms of analysis. As a bioinformatician using R,  
>> I am particularly interested in comparisons in terms of analysis,  
>> data manipulation/storage in R, etc. We have some experience  
>> analyzing Illumina data but no experience with Solid data.
> For whatever its worth, we had someone from The Broad recently give a
> talk about some work he's been doing with RNA-seq.
> Near the beginning of the talk he had a slide with the number of
> machines they had from each platform, it broke down to something
> roughly like so (if I remember correctly):
> Illumina: ~ 90
> SOLiD: < 10
> 454 : < 10
> And he mentioned that the solid and 454 machines are just basically
> collecting dust.
> I don't really have enough experience with either platform to draw and
> judgements myself, but the guy giving the talk seemed pretty convinced
> and thought it was relevant to share.
> -steve
> -- 
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
> | Memorial Sloan-Kettering Cancer Center
> | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact
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