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Old 11-16-2009, 11:40 AM   #1
Location: delaware

Join Date: May 2008
Posts: 11
Default de novo assembly and Illumina read length

We are preparing to do paired-end de novo sequencing on our GAIIx with the new kits. Is there a reason to run less than the maximum 100+ cycles on each end? There was a suggestion that the higher error rates at 100+ may make <100 cycles more desirable. My thoughts are more is better, particularly b/c a majority of the cost is linked to cluster generation.
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Old 11-16-2009, 11:15 PM   #2
Location: Udine (Italy)

Join Date: Jan 2009
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Originally Posted by bkingham View Post
My thoughts are more is better
This is usually true but if the more you produce is meaningless it is only a waste. For example one year ago we produce with the kit of 36 bases experiments of 45 bases with the result that we where oblige to throw away all the bases after the 36 ....

If the kit is able to produce 100 bases that you have to produce only 100 and be happy if all the 100 bases are of good quality and can be used

francesco.vezzi is offline   Reply With Quote

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