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?
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Ketil
For Illumina read cleaning I use FastQC that automatically check for primer/adapter contaminations
In particular, if you download and unzip the source distribution, you'll find the sequences in the Contaminants/contaminant_list.txt
You should ask the sequencing platform which performed the sequencing for the sequences of the primers and adapters that they used.
In this thread from seqanswers they link to this page
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 I worry that it is out of date, I identify very common high complexity k-tuples in my data with jellyfish (60K occurrences, in a 25x coverage data set), but no hits to any of these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.
Using the ncbi UNIVEC reference or similar, you can do a BLAST search against common artificial sequences.
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