Auto-q Qiime Analysis Automating Script Motivation: QIIME is a commonly used pipeline for microbiome data analysis. However, to run Qiime effectively and achieve its full capabilities, a large number of commands need to be typed and executed, which is a significant hurdle to those without a solid computing background. Results: A script named Auto-q was written in Python. It works as an interface to the Qiime cascade and produces all the results using only a single command. This script can be used to analyze paired-end FASTQ files produced by Illumina instruments with the following six steps: quality trimming, paired reads merging, chimera removal, quality control, OTU (Operational Taxonomy Units) picking, and diversity analyses. While it automates complicated workflows with reasonable defaults, most major analysis options can be also specified using command-line arguments or a configuration file. Availability: Auto-q is hosted at: https://github.com/Attayeb/auto-q Contact: attayeb@nibiohn.go.jp and kenji@nibiohn.go.jp This work was in part supported by grants from the Ministry of Health, Labour and Welfare of Japan and the Japan Agency for Medical Research and Development (16817372).