Other Scripts

Here are described scripts that are not part of the pipeline. For example They are run only once, to produce data to be used.

build_ASV_tree.r

Description

This script analyses the DNA sequances of all the ASVs in the data to create a phylogenetic tree. It saves it to a file as an r object (.rds) to be used in the future.

Input

output/ASV_full_taxa.csv: The phylogenetic classification of each microbial element sampled - contains the DNA sequance.

output

output/njs_distances_for_all_asvs_phylo.rds: An R object containing a naive tree produced using neighbor-joining from a distance matrix. output/fitted_asvs_phylo_tree.rds: An R object containing an optimized phylogenetic tree. It is an object of class 'pml'.