R Script – Filtering of 16S rRNA gene sequence counts and taxonomy of common contaminants from CROMO, California, USA CSW1.1 well depth profile May 2016

Script used for removing common contaminant taxa and counts from the original 16S rRNA gene sequence counts and taxonomy information from five depths in the CSW1.1 well at the Coast Range Ophiolite Microbial Observatory, California, USA collected during a one-day sampling event in May 2016. The script allows for filtering of common contaminants identified in Census of Deep Life samples as described previously by Sheik et al., 2018. Sequences identified as eukaryotes, archaea, mitochondria, chloroplasts, singletons, and unknown by SILVA were removed. After this, the script filters the dataset to remove taxa identified by Census of Deep Life to be common contaminants. Data was removed to better identify the relevant organisms present at each depth in the profile.