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README.md

Tutorials for metabarcode analysis

In this repository, you will find a set of tutorials of metabarcode analyses using different approaches

How to use

Download and uncompress

  • The whole set of tutorials from the download link (top-right above file list)

Install the following software :

install.packages("readr")     # To read and write files
install.packages("readxl")    # To read excel files

install.packages("dplyr")     # To manipulate dataframes
install.packages("tibble")    # To work with data frames
install.packages("tidyr")     # To work with data frames

install.packages("stringr")   # To manipulate strings

install.packages("ggplot2")   # To do plots


source("https://bioconductor.org/biocLite.R")
biocLite('dada2')             # metabarcode data analysis
biocLite('phyloseq')          # metabarcode data analysis
biocLite('Biostrings')        # needed for fastq.geometry

Directory structure

  • /fastq : fastq files

  • /dada2 : dada2 processed files

  • /databases : PR2 database files (contains PR2 database formatted for dada2 and mothur - https://github.com/pr2database/pr2database/releases/)

  • /img : Images

  • /R_dada2 : Dada2 tutorial for Illumina files

  • /mothur/454 : Mothur Tutorial for 454 files

  • /mothur/illumina : Mothur Tutorial for Illumina files

Short introduction to tutorials

Step by step instructions

Issues or questions

Please post here

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