Tourmaline

Tourmaline is an amplicon sequence processing workflow for Illumina sequence data that uses QIIME 2 and the software packages it wraps. Tourmaline manages commands, inputs, and outputs using the Snakemake workflow management system.

This version (Tourmaline-MMB-UMCU) is an adaptation of Tourmaline developed specifically for the Medical Microbiology Department at the UMC Utrecht. The Tourmaline-MMB-UMCU has been adapted for the use of the 16S rRNA dual-index primers as developed by Fadrosh et al. (Microbiome, 2014) and uses not yet demultiplexed fastq files as input.

Getting Started

The Quick Start Guide is a great place to start, containing short descriptions of the different steps needed to run the pipeline along with some example commands. In case you have multiple sequencing runs that you would like to merge, jump to Merging Sequencing Runs.

Citing Tourmaline

The Tourmaline paper is published in GigaScience:

Thompson, L. R., Anderson, S. R., Den Uyl, P. A., Patin, N. V., Lim, S. J., 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, https://doi.org/10.1093/gigascience/giac066