This repository contains detailed description and ready-to-run in mothur as batch files READMEs for processing ITS (fungi) and 16S rRNA (bacteria) amplicon sequencing data (MiSeq), with a few additional files.

It also contains (interactive) R scripts for the initial downstream analysis of the mothur processed data.

The folder /16S_mock_mothur_output_phyloseq_input contains the results of processing in mothur sequencing data for three 16S MOCK samples. These files can be directly used in "analysis_16S_v1.R".

The folder /data contains reducted files (70-80% to the original size of read files that were used to produce result files in /16S_mock_mothur_output_phyloseq_input) of sequencing reads for one ITS and three 16S MOCK samples that can be used to test the procedures provided here.