Forward and reverse reads overlap but don't align properly

[ddavis]

I am working with Archaea F and R reads acquired with the 344f and 915r primers. Each read is 300bp long so there is overlap but it is only 29 bp. I want to pair-end align the reads using PEAR or a program similar to it, but a past paper (https://onlinelibrary.wiley.com/doi/...1111/geb.12670) indicated that the length of the amplicon made it unable to align properly.

What's the best way to troubleshoot this? Is there another program that works for this instance or should I just use the F and R reads separately?

Thanks for the help.

[Bukowski]

Chances are the overlap isn't enough with the quality of the 600 cycle kits and any quality trimming in a pipeline, the normal recommendation is just to use the F reads as these are higher quality.