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  • How to get sequences of Illumina sequencing reagents/spike ins?

    Forgive my ignorance, I am not sure if this is a 'real thing' or if it is of any importance.

    I have the sequences of the indexed adapters we use as well as the PCR primers/oligos for library preparation, but I am not sure of any reagents or primers that go into the mix for sequencing.

    How would I find sequences and/or fasta files for whatever non-sample DNA/oligos such as spike ins or other 'contaminants' (with respect to the reads) may be going into the HiSeq rapid run? Thank you.

  • #2
    hi ronton,
    Its not clear what your intention is, but this might help you -
    Oligonucleotide (oligo) sequences of Illumina adapters used in AmpliSeq, Nextera, TruSeq, and TruSight library prep kits.

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    • #3
      This is perfect, thank you. The goal is for adapter/contaminant trimming/removal. I am a newbie working my way through sequence analysis.

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      • #4
        Other sequences that you might consider is from PhiX genome library which is recommended to be spiked-in in all sequencing runs for troubleshooting and other purposes. These will appear as reads. Here is a web page with links to genome sequence of PhiX: http://support.illumina.com/sequenci...e/igenome.html

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