SOLiD v3 vs Solexa

[coonya]

Hi.

Are there anybody who use SOLiD v3 and solexa sequencers?

I just want to know that SOliD v3 system have a problems and what's the disadvantage of SoliD compare with Solexa.

Thank you.

[westerman]

SOLiD v.3 is rather new technology. It is just being rolled out (we may ours by the end of the month). I doubt if you will much feedback on how SOLiD v.3 works much less a comparison of Solexa versus SOLiD v.3.

My gut level feeling -- not having either platform -- is that Solexa is easier to set up and run on the laboratory side. SOLiD v.3 with 50 base paired reads will be very nice. Lots of data that can, maybe, be de-novo aligned.

[Chipper]

Any specific concerns? SOLiD v3 seems to be much improved in handling (labwise) compared to v2, not sure how it compares to Illumina. Sample preps are similar, not yet automated on either system. SOLiD will give more reads per run (2 slides, currently around 100 000 000 aligned reads per slide seems normal) but Illumina can do longer reads (> 100 bases reported).

[NextGenSeq]

SOLiD v3 was released in February 2009 thus every comparison study to date was done using older versions.

The Genome Analyzer is up to version IIx and was also upgraded this year.

Both Illumina and ABI are claiming that they will get over 90Gb of sequence data by the end of the year.

[westerman]

Any specific concerns? SOLiD v3 seems to be much improved in handling (labwise) compared to v2 ...

No specific concerns since we have yet to do the lab work for an actual v.3 run. v.3 is suppose to be more simple ... but there is a long way between "suppose to" and "really acts like".

I hope to be able to report some limited real-life experience in a month or so.

[jOn]

No specific concerns since we have yet to do the lab work for an actual v.3 run. v.3 is suppose to be more simple ... but there is a long way between "suppose to" and "really acts like".

I hope to be able to report some limited real-life experience in a month or so.

Hi westerman, I was just wondering if you'd had any experiences that you could feed back relating to this link. We currently have a 454 and are debating on what platform to invest in next. Any feedback you could offer would be great.

[westerman]

Hi westerman, I was just wondering if you'd had any experiences that you could feed back relating to this link. We currently have a 454 and are debating on what platform to invest in next. Any feedback you could offer would be great.

The lab people do like the v.3 chemistry more than v.2. On the informatics side having 300 million 50 base pair mate reads is really nice to have. One could envision being close to de-novo assembly. I am not that enthused about the Corona lite software that ABI/LifeTech provides but it does do a lot -- SNP calling, Indels, transcriptomes, etc. Additionally there have sprung up other programs that deal with the SOLiD's color-space data format; these programs may provide easier or better results than Corona Lite. Support from ABI is generally good.

As for which platform would be better -- Solexa or SOLiD -- I can not really comment on since we do not have a Solexa. I recall reading that there are more Solexas out in the field than SOLiD machines but that could just be due to a first-arrival-on-the-scene scenario.

[jOn]

Many thanks - that member# of yours is pretty Rock n Roll too.