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Old 12-14-2009, 07:38 AM   #1
seqAll
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Default read length of SOLiD and Solexa

Hi there,

What is the current read length of SOLiD and Solexa? And will it be increasing in the near future? I am looking for one able to do 150 bp.

Thanks!
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Old 12-14-2009, 08:06 AM   #2
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My understanding (not being a LifeTech person) is that SOLiD is 50 bp and is likely not to increase in the near future. Instead the SOLiD will concentrate on increasing the number of reads. For what the SOLiD is particularly suited for -- SNP and indel discovery -- this focus makes sense.

If you need longer reads than Solexa would be your choice. Or Roche/454 if you needs 300+ bp reads.
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Old 12-15-2009, 03:31 AM   #3
seqAll
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Thank you for the information.

It sounds like SOLiD will focus on short read. What is the length of Solexa? Illumina website says 75 bp x 2. Does it mean that it is suitable for my samples (about 100 bp - 200 bp)?
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Old 12-15-2009, 04:07 AM   #4
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Quote:
Originally Posted by seqAll View Post
Thank you for the information.

It sounds like SOLiD will focus on short read. What is the length of Solexa? Illumina website says 75 bp x 2. Does it mean that it is suitable for my samples (about 100 bp - 200 bp)?
"75 bp x 2" means it could sequence 75 bases on either end of your 100-200 bp templates. So for any template up to about 150 bases you would have sequence of the entire template, or nearly so. For templates larger than 150 bases you would have a sequence gap in the middle of your sequence.

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Old 12-15-2009, 06:02 AM   #5
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Illumina now officially supports 100bp x 2 paired end runs.
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Old 12-15-2009, 04:56 PM   #6
seqAll
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Thank you Phillip and kmcarr!

I have checked its website again, "The Genome Analyzer IIx offers a unique combination of 2 x 100 bp read length and >300 million reads per flow cell..."

That is amazing!
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Old 12-15-2009, 05:11 PM   #7
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I have seen a presentation where Illumina showed some data from internal testing on their latest machine that were PE 2X125bp runs. The higher error rates towards the ends are partially compensated for by the overlapping reads in the middle 50bp.
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Old 12-16-2009, 05:01 AM   #8
pmiguel
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Quote:
Originally Posted by seqAll View Post
Thank you Phillip and kmcarr!

I have checked its website again, "The Genome Analyzer IIx offers a unique combination of 2 x 100 bp read length and >300 million reads per flow cell..."

That is amazing!
Yeah that would be 60 gigabases.

Are there IIx machines capable of this throughput in the field now? Looking at NCGR's info, looks like looks like you would expect 120 million passing reads if you used 10 lanes. (Maybe 9 lanes/flow cell would be more accurate?) So 300 million is a major difference.

How many reads/lane are people getting on the Solexa?

Spec for the SOLiD running at version 3.5 is 500 million raw reads/flow cell. For a decent run maybe 2/3rds will be mappable. Read length is 50 (x2 for a mate pair run). Two flow cells per instrument. 100 gigabases of raw sequence. Maybe 60 gigabases mappable. About 2 weeks to run. Pushing 4-5 gigabase/day.

That is spec. We just got the 3+ upgrade. Will try it out soon, I hope. But there are version 3.5 instruments in the field now that have completed runs.

If that Solexa figure of 300 million reads/run is in house only, then we would want to compare it to SOLiD version 4 projected stats: which would be around 80 gigabases.

Well, that would be for a 2x50 tag runs. At the last User's Summit AB was threatening to release paired-end chemistry. So you could have a mate-pair run that did paired end on each insert as well. Effectively 2x50 + 2x35.

But probably best to just compare what is in the field now. Who knows what we will see 3-6 months from now?

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Old 12-16-2009, 05:50 AM   #9
Xi Wang
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Do anybody know how is progress of single molecule sequencing technologies? I guess it will amaze us more in the near future.
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