Qiime2 to Phyloseq
The purpose of this post is to demostrate a workflow to convert Qiime2 objects for use in Phyloseq within an R environment. All the data and scripts can be found at my Github \\ Qiime2_to_Phyloseq Qiime2_to_Phyloseq Cody Glickman 10/26/2018 Purpose This script details the steps to convert qiime2 objects into a Phyloseq object. The workflow of processing data with Qiime2 can be found at the Moving Pictures tutorial. This script is adapted from Pedro J. Torres. All the data and scripts can be found at my Github Requirements Qiime2 artifacts needed to convert for phyloseq analysis: Metadata/Mapping File Table File (.qza) Taxonomy File (.qza) Tree File (.qza) {Optional} Convert Qiime2 qza on Command Line The chunk below contains commands executed on the command line. Qiime should be installed and in your path. Otherwise the commands can be copied and pasted into the terminal running a qiime environment