Adapter/Linker/Primer Sequence Database?

Question

[Ketil]

I want to QC some data to check for synthetic sequences - primers, adapters, etc. So I went to look for a downloadable fasta file, in my case for Illumina sequencing. But I am unable to find this. Clearly, this is a tremendously useful thing to have, so I'm probably just looking in the wrong places - obviously Illumina makes this available somewhere.

But I just can't find it. Help?

Answer 1

[Frédéric Bigey]

For Illumina read cleaning I use FastQC that automatically check for primer/adapter contaminations

[Steve Lianoglou]

In particular, if you download and unzip the source distribution, you'll find the sequences in the Contaminants/contaminant_list.txt

Answer 2

[helene.badouin]

You should ask the sequencing platform which performed the sequencing for the sequences of the primers and adapters that they used.

Answer 3

[Irsan]

In this thread from seqanswers they link to this page

[Ketil]

Yes, I found this. I worry that it is out of date, I identify very common high complexity k-tuples in my data with jellyfish (60K occurrences, in a 25x coverage data set), but no hits to any of these sequences. Anyway, I wrapped those in FASTA (which makes them useful for those of us who don't process sequences in Word and Excel), you can download it here if you want.

http://malde.org/~ketil/illumina-adapters.fasta

Answer 4

[eric.kern13]

Using the ncbi UNIVEC reference or similar, you can do a BLAST search against common artificial sequences.

https://www.ncbi.nlm.nih.gov/tools/vecscreen/univec/