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

Kasper Daniel Hansen khansen at stat.berkeley.edu
Wed Dec 23 18:46:26 CET 2009

On Dec 23, 2009, at 2:16 AM, Sulev Kõks wrote:

> Hi,
> 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.

This is not true.  I know of at least two library preps for Illumina that preserve strandedness.

> 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.

There is a big difference between labs regarding how many reads they get.  The market moves pretty fast.  I am not too sure that SOLiD produces the most reads right now.  And as far as I know they produce shorter reads, which is critical for some applications.

> 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.

One major difference is that most tools right now operate directly on FASTQ files.  This means that they do not operate in colorspace, and a big (possible) advantage of the SOLiD platform is lost.  If you are in a lab with substantial bioinformatics resources this might not be a problem, because you can work around it.  But if not, the selection of tools for the SOLiD platform is - in my impression - much smaller.  And analysis is quickly becoming the the bottleneck for these types of data.


> Cheers
> Sulev
> 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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