Category: phyloseq

Import DADA2 ASV Tables into phyloseq

ASV Tables Created in R

ASV tables created using the Bioconductor/R version of DADA2 are matrix files with samples as rows and taxa as columns. The taxa names are the sequences themselves. Because these matrices can be quite large they are most conveniently saved as compressed rds files. Read these files into R and create an experiment level phyloseq object containing an OTU or ASV table and representative sequences with the following R script: Continue reading “Import DADA2 ASV Tables into phyloseq”

Rooting Unifrac Trees in phyloseq Objects

The method of rooting trees described in the post “Unifrac and Tree Roots” is now included in QsRutils beginning with version 0.3.2 as function root_phyloseq_tree. Given a phyloseq object with an unrooted tree, it returns the same type of phyloseq object with the tree rooted by the longest terminal branch.

Unifrac and Tree Roots

Unifrac distances have the attraction of including phylogenetic relatedness, based on a tree of the representative sequences, in the distances among samples calculated from an OTU table. FastTree is the usual method of choice in generating the tree, although USEARCH also provides a method. Both methods calculate unrooted trees, and calculation of Unifrac distances requires a rooted tree. The problem arises in how to best root the tree. I found a discussion of the problem on the phyloseq GitHub site (https://github.com/joey711/phyloseq/issues/597). Continue reading “Unifrac and Tree Roots”