Anybody having Nextseq 2000 600cycle kit issues. Drop of Q score around 100 cycles and poor read 2 quality.
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I'm having trouble uploading the Q30 plot from our most recent 2x300 run on the NS2K, but average Q30 across the entire run was 88.77 (82.76 for just R2), and Illumina states an average %Q30 or greater of 85%+ so no issues there.
A drop shortly after 100 cycles could indicate adapter dimers clustering and losing signal quality after read through. Can you share any more information about your run like the library type, some tapestation/BioA traces, %base composition plot from the run?
Our last run of this type was in May, reagent cartridge lot was 20938598. -
Yes, we recently started having issues with our 16S runs on 600cyc kits, where we are seeing seemingly random sharp decreases in quality in the middle of Read 2, just for a single cycle. Also seeing dramatic quality drop-off at the end of Read 2, way more than usual. Our 300 cyc kits on WGS libraries seem fine.
Did you ever figure out what was going on with your runs? We've been doing this for years and haven't changed anything about our library prep process, so we are wondering whether it could be a sequencing reagent/flow cell batch issue, or perhaps a problem with the software update that a field tech did right before things went sideways.Comment
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We've been having some trouble with the 300 cycle P4 kits. We received our NextSeq2000 early Nov. 2025. First run had fewer clusters passing filter and what looked like a dead spot on the flow cell, so FAS had us repeat. Repeat run still had PF under spec, and Illumina said it looked like an optics issue. Engineer on site adjusting optics (?) and cleaning the thermal plate. She also upgraded software.
Third run, we see %Q30 drop around cycle 140 in lane 2 and around cycle 230 in lane 1.
Fourth run, we accidentally left the cartridge at room temp for 23 hours. Ran anyway, great data output.
Fifth run, we see %Q30 drop at cycle 162 in lane 1 with lane 2 unaffected.
Sent our library to Illumina and they ran it successfully using a reagent cartridge and flow cell we had.
We have had three successful P1 300cycle runs, and so far no issues with those kits.
Illumina is maintaining its a library or consumables issue, and that the instrument is fine, and want us to continue troubleshooting the P4 with new libraries.
Has anyone gotten any resolution with their quality issues?Comment
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