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Oligo Sequences

Archive: Roche 454 
Archive: ABI SOLiD & Life Tech 5500XL
Illumina 

rRNA bacterial gene and ITS fungal metagenomics primers

Blunt-end ligation with PCR addition of indexes

Some simple commands to use to search for adaptor-dimers:
In Illumina data:

grep -c GATCGGAAGA <filename.fastq>

This works for a standard Illumina genomic DNA library made with TruSeq V3 Y adaptors, and since the Y adaptors are RC's on each end, works equally well for read 1 and read 2.

For small-rna library/single stranded RNA library, The previous command will work for read 1. For read 2, use something like:

grep -c ATCGTCGGAC <filename.fastq>
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