Question: Adapter/Linker/Primer Sequence Database?
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gravatar for Ketil
6.0 years ago by
Ketil3.9k
Germany
Ketil3.9k wrote:

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?

fasta illumina adaptor • 4.5k views
ADD COMMENTlink modified 3 months ago by eric.kern13120 • written 6.0 years ago by Ketil3.9k
2
gravatar for Frédéric Bigey
6.0 years ago by
Montpellier, France
Frédéric Bigey280 wrote:

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

ADD COMMENTlink written 6.0 years ago by Frédéric Bigey280
4

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

ADD REPLYlink written 6.0 years ago by Steve Lianoglou4.9k
1
gravatar for helene.badouin
6.0 years ago by
University Paris South
helene.badouin20 wrote:

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

ADD COMMENTlink written 6.0 years ago by helene.badouin20
0
gravatar for Irsan
6.0 years ago by
Irsan6.8k
Amsterdam
Irsan6.8k wrote:

In this thread from seqanswers they link to this page

ADD COMMENTlink written 6.0 years ago by Irsan6.8k
1

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 I worry that it is out of date, I identify very common high complexity k-tuples in my data with jellyfish (60K occurrences, in a 25x coverage data set), but no hits to any of these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

ADD REPLYlink written 6.0 years ago by Ketil3.9k
0
gravatar for eric.kern13
3 months ago by
eric.kern13120
United States
eric.kern13120 wrote:

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/

ADD COMMENTlink written 3 months ago by eric.kern13120
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