No active work is currently being done on this branch, except very rare bug fixes. For up-to-date workflows, see https://github.com/ctmrbio/ctmr-amplicon
A few guides in how to use our tools, and some other people's tools as well. All scripts mentioned in the tutorials are also included in this folder.
Amplicons_overlap will teach you how to use Usearch to process amplicon libraries where the forward and reverse sequencing reads overlap.
Amplicons_no-overlap does the same for the case where the reads don't (or rarely) overlap. This one is more convoluted, so do try to get overlaps.