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Phyloseq workflow for microbial community analysis

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posted on 09.02.2020 by Jarrod Scott
Complete, fully reproducible phyloseq workflow for 16S rRNA microbiome analysis of the Bocas del Toro hypoxic event. Included are the HTML and Rmarkdown (.Rmd) files plus the output of the DADA2 pipeline in Rdata format which is the main input file for the phyloseq workflow.
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.
The MANUAL_INPUT.zip directory contains all of the additional input files (mainly tables) necessary to run this workflow. Please note script will create a directory called R_OUTPUT wherever the .Rmd file was called from. This is where the script will store output files.

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