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Old 02-27-2017, 07:57 AM   #103
dsobral
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Location: Lisbon, Portugal

Join Date: Jan 2012
Posts: 21
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Just to add our 2 cents.

We have a MiSeq running since 2013, and after some hickups we're now stable with it and reasonably happy.

We just recently installed a NextSeq500 and our first tests are not great. Q30 is >80%, but there are many low quality bases (constantly Q=14 "/"), and the worst part is that instead of being towards the end, they seem a bit randomly distributed. When comparing PhiX in a 2x150bp NextSeq with a 2x250bp MiSeq, after alignment I see a 0.2-0.3% error rate with MiSeq and 0.9-1% error rate with NextSeq (1M sampled reads). In the "randomly" distributed Q=14 bases I seem to notice more A to T transitions, but I didn't have time to gather more systematic statistics... If I do quality trim on the MiSeq I can easily get higher quality data, with the NextSeq since its randomly distributed is harder...

We've complained to the Illumina people, let's see what they say...
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