Directory content

This sub-directory contains the following child directories:

• /ASV_tables

• /taxonomy

• /statistics

The ASV_tables directory contains the filtering tables used to clean and decontaminated the ASV tables generated by the DADA2 pipeline. The taxonomy directory contains the UNITE .fasta file necessary (not on GitHub) to complete taxonomic assignments of the ASVs. The files in ASV_tables and taxonomy stem from the mim2_bioinformatics.qmd notebook. The statistics directory contains the the .csv and .rds files used to complete statistical analyses for the project in the mim2_statistics.qmd notebook.

Important files resulting from the pipeline

• asv_10 == clean_data/ASV_tables/ASVs_8450_cleaned_10_percent.rds
• ps_clean_3 == clean_data/taxonomy/TAXA_8450_phyloseq_nonsingletons.rds
• ps_clean_3_df == clean_data/taxonomy/TAXA_8450_phyloseq_nonsingletons.csv

BAR 2024-05-23