QIIME 2 Pipeline for metagenomics analysis

Instroduction

Dependencies

This pipeline has been used in MacOS Sonoma 14.3 and Ubuntu 23.

Install in order:

• QIIME 2 v2023.2
• Dokdo v1.16.0 (Install inside QIIME2 environment)
• PICRUst2 v2.5.2 (Install inside QIIME2 environment)

How to use

The pipeline is localted in qiime-pipeline.sh, a Bash script where its general use can be called as:

./qiime-pipeline.sh -ipfdtceabkq && \
                            PATH_TO_FASTQ_FOLDER && \
                            REGION && \
                            DENOISE_ALGORITHM && \
                            DENOISE_CUT && \
                            COLLAPSE_LEVEL

Project structure