Tutorials for metabarcode analysis

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

• Mothur
  • 454 data
  • Illumina data
• Dada2
  • Illumina data

How to use

Download and uncompress

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

Install the following software :

• Terminal program. For Windows MobaXterm is highly recommended : https://mobaxterm.mobatek.net/

• Notepad++ if you are using windows : https://notepad-plus-plus.org/

• mothur : https://github.com/mothur/mothur/releases/tag/v1.39.5

• R : https://pbil.univ-lyon1.fr/CRAN/

• R studio : https://www.rstudio.com/products/rstudio/download/#download

• Download and install the following libraries by running under R studio the following lines

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

• Dada2 Illumina

Step by step instructions

• Mothur 454
• Mothur Illumina
• R Dada2 Illumina
• Compare analysis with mothur vs. dada2

Issues or questions

Please post here