Built Environment Meta-Analysis

RI Adams, AC Bateman, HM Bik, JF Meadow

This repository contains data and scipts that were used to conduct a meta-analysis of 16 high-throughput sequence datasets from built environments around the world. The analysis also includes 7 putative source environments.

• merged_datasets contains the main OTU tables (in biom format) that were used during the analyis.
• individual_biom_tables contains lots of individual OTU tables from each individual study. These were tied together using the script mergeOTUTables.sh. This folder also contains the stats from the resulting merged otu table.
• fungi contains an OTU table, a mapping file, and an ordination output. We did not find enough studies to conduct a meaningful analysis for fungi, so this folder is included just for posterity.
• pinch_biom_tables We used the phinch online platform for extensive data exploration. The biom tables in this folder already have metadata embedded to use directly in phinch.
• R Almost all analysis and figure generation happened in R. This folder contains scripts in RMarkdown format. All data should be included to rerun and further explore the analysis we carried out.
• scripts contains the pickTheseOTUs.sh script that was used to generate OTU tables from raw sequence files. We processed all datasets with identical parameters using this script. This also contains a few of the QIIME commands we used to generate some preliminary analysis.

This study is currently in review.