National-Workshop-Microbiome-Informatics

Introduction

This workshop will help the newbies to learn how to analyse the 16s rRNA amplicon data using R.

Pre-requisities

R should be installed in the user system/PC. R installation steps are given in https://cran.r-project.org/bin/windows/base/R-4.4.1-win.exe.

RStudio should also be installed, https://download1.rstudio.org/electron/windows/RStudio-2024.04.2-764.exe

The following R packages are required for the analysis the 16s rRNA amplicon data:

R packages

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")

BiocManager::install("dada2")

BiocManager::install("phyloseq")

install.packages("microeco")

install.packages("microeco")

install.packages("ggplot2")

install.packages("ggpubr")

install.packages("ggdendro")

Workflow

Raw FASTQ files and reference taxonomy file (Silva_138)

Download amplicon sequencing raw data (.zip) files for analyses, following this link: https://github.com/RoyDibakar/National-Workshop-Microbiome-Informatics/archive/refs/heads/main.zip

Download the reference taxonomy file using the following link : https://zenodo.org/records/4587955/files/silva_nr99_v138.1_train_set.fa.gz

Unzip the folder; keep the reference taxonomy file and the FASTQ files in the same folder

The R codes can be downloded from the following link https://github.com/RoyDibakar/National-Workshop-Microbiome-Informatics/blob/main/Codes_Microbiome_Informatics.R

Team

Dibakar Roy, Paramita Roy, and Sudipto Saha