[Biopython] Adaptor trimmer and dimers

[natassa]

Hallo Biopythoners, 
I followed a recent thread conversation about adaptor trimming, which I intend to do on Illumina runs, and I am not sure I know where exactly in github I could find Brad Chapman's code for trimming AFTER modifications that he has done based on the thread conversation. I d like to test that code, which looks very appealing to me if it computes a global alignment and allows for a certain simplicity, ex number of mismatches. The link in BradChapman's original post on the trimmer points to a non-Biopython Github (sorry if i understand bad those things!) and I have the impression it is not updated for the above (and other) features discussed in the thread.

On the same topic, I would like to ask people's experience on the detection of adaptor dimers. I have just started considering the issue, and my understanding is that Illumina technology at least is mostly biased for the presence of adapter dimers, rather than adapter fragments within the reads. This was confirmed by the company who did the sequencing for my samples. So I was surprised to find no discussion on dimers or no obvious adaptation on scripts for their detection. Maybe i am wrong?
I tested a perl script that detects 'adapter-only sequences' but when i tried to visually inspect those to see if they represent dimers, I realized the importance of doing a global alignment ;-), the script doing a local one. The fraction of the adapter-only sequences, if those represented the dimers I am looking for, is small, so i d be happy to filter them out. But I am not sure for this, and lacking a way to detect such dimers, I would happily give a go to a trimmer, not a very aggressive one!
Do you think adapter trimming is critical? What fractions of your illumina reads contained adapters?
Sorry for the overflow of questions!
Many thanks, 
Anastasia 
Anastasia Gioti
Post-Doc, Evolutionary Biology Department
Upssala University
Norbyvägen 18D
SE-752 36  UPPSALA
anastasia.gioti at ebc.uu.se
Tel: +46-18-471 2837
Fax: +46-18-471 6310