Tutorial output for Tourmaline amplicon sequence processing workflow

Tutorial output for the Tourmaline amplicon sequence processing workflow.

Tourmaline was run on the test data provided in the directory 00-data, which were downloaded along with the rest of the repository using this command:

git clone https://github.com/aomlomics/tourmaline

Reference data were downloaded and symlinked using these commands:

cd tourmaline/01-imported
wget https://data.qiime2.org/2021.2/common/silva-138-99-seqs-515-806.qza
wget https://data.qiime2.org/2021.2/common/silva-138-99-tax-515-806.qza
ln -s silva-138-99-seqs-515-806.qza refseqs.qza
ln -s silva-138-99-tax-515-806.qza reftax.qza

Paths in 00-data/manifest_pe.csv and 00-data/manifest_se.csv were edited to match the local paths.

Output for all modes of the workflow were then generated in series:

conda activate qiime2-2021.2
snakemake dada2_pe_report_unfiltered
snakemake dada2_pe_report_filtered
snakemake dada2_se_report_unfiltered
snakemake dada2_se_report_filtered
snakemake deblur_se_report_unfiltered
snakemake deblur_se_report_filtered