Phyloseq workflow for microbial community analysis

Complete, fully reproducible phyloseq workflow for microbiome analysis of herbivorous reef fish. Included are the HTML and Rmarkdown (.Rmd) files plus the output of the DADA2 pipeline in Rdata format which is the only input file for the phyloseq workflow.<br>Sequences were filtered, and dereplicated. Sequence variants were called and putative chimeras identified. Sequence variants were classified using SILVA and GreenGenes databases. File contains a sequence table and taxonomy table. We imported this file directly into phyloseq for community analysis. <br>Also included are the full sequence and taxonomy tables for all 12,479 ASVs. These tables contain data before removing mitochondria and chloroplasts ASV. Also included are data for the three samples that were not part of the original analysis.--The taxonomy table contains the complete SILVA lineage plus the actual sequence for each ASV. --The sequence table contains the raw read count for each ASV by sample. <br><br><br>