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Old 01-25-2018, 08:17 AM   #1
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Location: Germany, Bochum

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Default Illumina fusion primers - Nextera or TruSeq based?

Dear all,

We have been using (old version) TruSeq fusion primers (Illumina flow cell bind, + sequencing primer bind + inline tag + amplification primer) for a while and would now like to add indexing to the P5 and P7 to pool more samples on the same run (Elbrecht Leese in the pictures). When looking into this, we discovered that:

1) We are using a wrong sequences on the P7 (Rd1 SP)
2) When looking at published fusion primer system, mostly TruSeq and Nextera are used (see pictures). But what really confuses us, it that the sequences in the nextera and truseq bases systems are very different! How can this be?

This is really confusion, because I always thought there is one standard index read set included with illumina sequencers, but the different sequences would indicate that for one system custom sequencing primers would have to be added? Am I missing something here?

We would like to have a ready to load fusion primer system, that uses indexing from illumina without the need to provide custom sequencing primers / and that works on all illumina systems (especially MiSeq and HiSeq rapid run). Any advide which (TruSeq or Nexters) to choose here?

What are the advantages of each when used as a one step fusion primer? Both seems to be used in the literature. OR to ask the question differently, what are the actual standard sequencing / indexing primers used, and do they differ between instruments?

Thanks every one = )

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