This QIIME2 SnakeMake pipeline has been adapted from: https://github.com/shu251/tagseq-qiime2-snakemake
Any use should cite the tagseq-qiime2-snakemake repo and tutorial in addition to this repository and the snakemake software.
USAGE:
Configure the script with parameters and a path to your sequences by editing the config.yaml file.
Install snakemake into a conda environment. See here: for installation instructions. https://snakemake.readthedocs.io/en/stable/getting_started/installation.html
Run the script using the command
-s snakefile-import summarize
first to import and summarize sequences.
Next, use
snakemake -s Snakefile-16S-18S-TA
to run the remainder of the pipeline after setting quality parameters based on the output of step 1.