This folder contains scripts used to perform QIIME2 analysis on the 16S rRNA amplicon data, the QIIME2 output artifacts, and the Rmd script to reproduce the figures in the manuscript.
Software used: QIIME2 v2020.4 and R v3.4.1
QIIME2 bash script and Rmd files
- 00_qiime2_alltogether.sh: Main QIIME2 script with all commands
- Loperamide16Samplicon_analysis.Rmd and knitted outputs
QIIME2 artifacts and processed files
- core-metrics-results: diversity metrics calculated by QIIME2
- exported: files exported from QIIME2, then imported to excel
- rarefaction: curves generated by QIIME2
- taxonomy: annotations and barplots generated by QIIME2
- all other qza and qzv files generated during the QIIME2 pipeline
Output from Rmd file in scripts/
Each file is named according to the manuscript figure
- Loperamide16Samplicon_manifest.txt - file to import raw sequence files into QIIME2 .qza format using
qiime tools import - Loperamide16Samplicon_metadata.txt - metadata file formatted for QIIME2 import during
qiime feature-table summarize - PRJNA908751_NCBI_info.xlsx - corresponding accession numbers for each 16S rRNA amplicon sample files