In this repository, you will find a set of tutorials of metabarcode analyses using different approaches
- Mothur
- Dada2
- The whole set of tutorials from the download link (top-right above file list)
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Terminal program. For Windows MobaXterm is highly recommended : https://mobaxterm.mobatek.net/
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Notepad++ if you are using windows : https://notepad-plus-plus.org/
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mothur : https://github.com/mothur/mothur/releases/tag/v1.39.5
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R studio : https://www.rstudio.com/products/rstudio/download/#download
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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
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/fastq : fastq files
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/dada2 : dada2 processed files
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/databases : PR2 database files (contains PR2 database formatted for dada2 and mothur - https://github.com/pr2database/pr2database/releases/)
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/img : Images
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/R_dada2 : Dada2 tutorial for Illumina files
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/mothur/454 : Mothur Tutorial for 454 files
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/mothur/illumina : Mothur Tutorial for Illumina files
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