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Old 10-29-2010, 05:04 PM   #1
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Default Nextera vs Illumina Library Prep

Does anyone have any information about Nextera multiplex library prep versus the Illumina method?
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Old 11-02-2010, 07:24 AM   #2
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You should be able to find the information you need in the Nextera Illumina-compatible protocol (click the "protocol" link on the product page). Appendix A lists the sequences of our barcode primers; you can also design your own if you wish.

If you have any other questions or issues, feel free to contact me via PM.
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Old 12-30-2010, 10:58 AM   #3
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Default Multiplex prep

We used the Nextera multiplex primers to prepare several bacterial libraries, then pooled the libraries for one lane of Illumina sequencing. This was quite straightforward following the manufacturer's instructions. The libraries sequenced well and we could identify a perfect match to each 6 bp index sequence in 97% of the Illumina index reads. Be aware that if one is performing paired read sequencing, the second of the paired reads (actually Illumina read 3) will have low quality in the last 10-20bp because the index read (read 2) uses some of read 3's reagents. The read1 quality averaged Q20 out to 120 bp while Q20 was around base 110. We found the Nextera kit to be very, very simple and much faster compared to the standard Illumina prep, although we have not examined any potential read bias yet.

Last edited by Boonie; 12-30-2010 at 11:04 AM.
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