I am new to archaea specific amplification and am wondering if anyone has a specific primer set up for archaea to be sequenced using MiSeq with custom dual barcoding?
I have found that the best region with MiSeq may be the v3-v4(517F/958R) region (according to VAMPS) and wanted to know if I could use their suggested 16S archaea specific primers in place of the v4 bacterial primers used in the custom primer method outlined by Kozich and Schloss. In other words, could I use the same adapter-barcode-pad-linker-16Sprimer(F/R) sequences and only change the 16S specific primers (keeping in mind the Tm of course)?
I have also read the paper by Klindworth et al, 2012 suggesting the use of 349F/519R for Illumina sequencing, but I fear that this specific primer set may create sequences too short for MiSeq sequencing. I was unsucessful in finding other published papers that amplified archaea and sequences using MiSeq.
Any insight or suggestions would be greatly appreciated! Thank you.