Contaminant Filtering R Script

R script used to perform contaminant filtering of sequence data based on results from Shiek et al. (2018 ). Portions of code within were written by Katherine M. Fullerton (KMF) and utilized in work by Fullerton et al. (2021). Code comments indicate code written by KMF.Sheik et al. 2018 doi:10.3389/fmicb.2018.00840Fullerton et al. 2021 doi:10.1038/s41561-021-00725-0Also contains code that imports and combines BLAST results from species classifications and that subsets taxa that are closely related to the candidate Genus Serpentinomonas. Fasta file from the phyloseq object was used to BLAST these sequences against published sequence data for Serpentinomonas strains A1 and B1 to identify Serpentinonomas OTUs in the dataset.