Citation and Legacy v1

How to cite Tourmaline

Thompson, L. R., Anderson, S. R., Den Uyl, P. A., Patin, N. V., Sanderson, G. & Goodwin, K. D. Tourmaline: A containerized workflow for rapid and iterable amplicon sequence analysis using QIIME 2 and Snakemake. GigaScience, Volume 11, 2022, giac066. doi: 10.1093/gigascience/giac066

v2 vs v1 (high-level)

• v2 runs via tourmaline.sh, modular steps: qaqc, repseqs, taxonomy
• v2 allows starting from external inputs (QZA/BIOM/FASTA)
• v1 README contains detailed classic Snakemake rule usage and Docker notes

Legacy v1 resources

• V1 branch: https://github.com/aomlomics/tourmaline/tree/V1
• Old README: tourmaline/README_v1.md
• Some instructions (e.g., Docker options, legacy QIIME 2 versions) remain useful background.