Snakemake-based amplicon processing protocol for 16S and ITS sequences:
- Performs quality control based on quality, can trim adapters, and remove sequences matching a contaminant database;
- Handles paired-end read merging;
- Integrates de novo and reference-based chimera filtering;
- Clusters sequences and annotates using databases that are downloaded as needed;
- Generates standard outputs for these data like a newick tree, a tabular OTU table with taxonomy, and .biom.