Calvin Fung1, Mathew Rusling1, Thomas Lampeter2, Charles Love1, Anisha Karim1, Christian Bongiorno1, Li-Lian Yuan1,3. 1. Des Moines University, College of Osteopathic Medicine, Des Moines, Iowa. 2. New York Institute of Technology, College of Osteopathic Medicine, Old Westbury, New York. 3. Department of Physiology and Pharmacology, Des Moines University, College of Osteopathic Medicine, Des Moines, Iowa.
Abstract
QIIME is a widely used, open-source microbiome analysis software package that converts raw sequence data into interpretable visualizations and statistical results. QIIME2 has recently succeeded QIIME1, becoming the most updated platform. The protocols in this article describe our effort in automating core functions of QIIME2, using datasets available at docs.qiime2.org. While these specific examples are microbial 16S rRNA gene sequences, our automation can be easily applied to other types of QIIME2 analysis.
QIIME is a widely used, open-source microbiome analysis software package that converts raw sequence data into interpretable visualizations and statistical results. QIIME2 has recently succeeded QIIME1, becoming the most updated platform. The protocols in this article describe our effort in automating core functions of QIIME2, using datasets available at docs.qiime2.org. While these specific examples are microbial 16S rRNA gene sequences, our automation can be easily applied to other types of QIIME2 analysis.