/mimb_16S

Repository containing scripts and files for 16S gene community analysis chapter in Methods in Molecular Biology

Primary LanguageShell

MiMB_16S

Required Software

Before running through this tutorial, you must have QIIME2 installed and activated. This has been tested with the QIIME2 2018.4 release, available at https://qiime2.org.

Running the Scripts

Run scripts in this order:

  1. fetchFastq.sh
  • This script will fetch example data and metadata from EBI (~30mins)
  • Data from Permentier et al., 2016 (DOI: 10.1111/1744-7917.12381)
  1. qiimeCommands.sh
  • This script provides the commands for an entire QIIME analysis (~1hr 45mins)