Reference oligotypes from well known strains for mapping NGS sequences

[Marco Meola]

Hi,

Is reference-based oligotyping possible as well? I explain it a litte, I have a number of oligotypes for a specific gene X present in Species Y from well characterized and cultivated strains. 

I would like to map the sequences of gene X resulting from NGS analyses (Ion Torrent PGM) to the reference oligotypes of the cultivated strains. Is that option included in oligotype? If no, what approach would you suggest?

The remaining sequences that are not mapped to the reference oligotypes would be analysed following the standard approach of de novo oligotyping.

Thank you!

Marco

[Rodrigo Ortega]

Hello Marco,

Were you able to use your reference oligotypes using the oligotype software or using another approach? I would be very interested in knowing if you found a solution

Thank you,
Rodrigo

[Marco Meola]

Hi Rodrigo, 

I haven't tried any further, but still waiting for a hint or response by Eren. Either way, I think it would be useful to have reference oligotypes based on deposited good quality 16S for single species.