Documentation Contents

DOI bioconda-badge


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.

This workflow is built using Snakemake and makes use of Bioconda to install its dependencies.