16S-mini-project: A Shell repository from Molecular Biology and Bioinformatics Unit - Molecular Biology and Bioinformatics Unit

About Project

This project creates a workflow for 16SrRNA analysis for researchers.The 16S rRNA is a ribosomal RNA necessary for the synthesis of all prokaryotic proteins.To read more on this click here.

Sample data

Datasets used for this workflow can be found here. The Dataset metadata is found at this link, but we will be downloading the datasets and metadata automatically using the data-downloader script.

Collaborators

Tools Used

Phases	Tools Used	Purpose	Link
Phase 1	FASTQC	Quality check/plots and stats	Link
Phase 1	Trimmomatic	Trim and Filter reads	Link
Phase 1	UPARSE	Stitching paired reads	Link
Phase 1	UCHIME	Chimera detection	Link
Phase 2	UPARSE	OTU picking and Chimera removal	Link
Phase 2	QIIME2	Classification	Link
Phase 2	QIIME2	Alignment	Link
Phase 2	QIIME2	Create Phylogenetic tree	Link
Phase 3	QIIME2	Alpha diversity	Link
Phase 3	QIIME2	Beta Diversity	Link

Set Up And Installation

For you to be able to follow this workflow;

Clone this repository locally, then
```
 cd "path/to/project/16S-mini-project" && bash start.sh
```
Once you do this, sit back, relax and sip some coffee or water 😊, its going to take a while.
End to End 16S RNA analysis can also be done using Qiime2 feature tools only. This analysis produces different core metrics alpha and beta analyses as well as explores different microbial profiles by assigning taxonomies. To follow this kind route, activate the Qiime2-2020.8 environment, cd into Qiime2-E2E-Analysis and bash scripts/16srna-deblur.sh to do denoising using deblur or bash scripts/16srna-dada2.sh to denoise using dada2. The scripts follow a download of datasets to analysis end of Qiime2. Please ensure that you read the documentation for each of the scripts used before running them. The automatic manifest file maker was adapted from this repo The script that exports Qiime2 artifacts into objects that can be used with phyloseq was adopted from this tutorial. More information about importing dada2 artifacts into phyloseq can also be obtained from here.

Bugs

There are no known bugs, but incase of any feel free to reach any collaborators of this repository.

LICENSE

MIT