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Old 11-26-2015, 10:56 PM   #6
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

@bluepoison: I suggest you try adapter-removal using BBDuk and adapters.fa, and see if fastQC still detects overrepresented sequences. If not, everything should be fine! But if it does, you may have a new adapter sequence, so please reply in that case.

@turnersd: Unfortunately... there are a lot of new adapter indexes in the latest Illumina letter that you linked - dozens. They are for human-specific tests, like autism, cancer, and other possibly genetic disorders. And as always, Illumina makes no effort to indicate which indexes go with which adapters. So, it looks like a huge amount of effort now to make a complete set of Illumina adapter sequences complete with indexes.

JGI does not do any human sequencing, so none of that is relevant to us. But for everyone else out there - I really hope Illumina, or someone in the community, compiles a full list of the new human-specific adapter sequences. Because there are so many, and I have no way to empirically determine whether the new sequences are correct (since we don't use them), it's not really possible for me to generate them. Illumina would provide the full, indexed adapter-sequences for trimming if they had the slightest concern for their end users, which they unfortunately do not appear to have.

So far, it's not clear to me which adapters go with new indexes, or why they even need new indexes for cancer versus autism, etc. Seems like a marketing ploy. But probably the new indices only affect amplicon sequencing and are irrelevant to randomly-shared libraries.
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