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

[ronton]

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.

[amitm]

hi ronton,
Its not clear what your intention is, but this might help you -

http://support.illumina.com/downloads/illumina-customer-sequence-letter.html

[ronton]

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

[nucacidhunter]

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