README for the greengenes v13_8_99 reference files
Aug 12, 2014 • PD. Schloss •
2 min read
The greengenes developers periodically update their reference files on their ftp server. What follows is our process for generating a mothur-compatible set of files to generate a greengenes taxonomy reference of those sequences.
The original files are available from the greengenes ftp server:
We need to modify the 99_otu_taxonomy.txt taxonomy file to remove the spaces and labels such as "p__", "c__", "o__", "f__", "g__", "s__". We’ll do this with R: