Welcome to the 16S-rRNA-Analysis wiki!

With this pipeline we can develop a full 16S rRNA analysis with Qiime2 (2019.7) (I always worked with hipervariable regions V3-V4) for microbial characterization.

After that, with some of these results you can perform the phylosimbiotic and cophylogenetic analysis (for Phylosymbiosis and Co-evolution models). You will learn to:

1. Decompress your files .tar and Import your sequences in Qiime2.
2. Demultiplex
3. Quality Filter analysis with DADA2.
4. Features table construction

   OTUs table

5. Alpha-rarefaction plotting
6. Alpha-Beta diversity Analysis
   • Alpha diversity

     chao1, simpson, shannon, margalef index

   • Beta diversity

     Bray-Curtis, Weighted, Unweighted-Unifrac

7. Taxonomic classification
8. Construct a phylogeny
9. Classifiers

   Random Forest

10. Graphics Bray-Curtis PCoA Taxonomic barplots Creating a tree (ML) or a midpoint rooted tree. Heatmaps
11. Export final-files

    With Qiime1

First, you need to check that you have:

• Installed qiime2 and qiime1 at your HPC cluster
• Load a conda environment module load anaconda/python3.7
• Activate qiime2 source source activate qiime2-2019.7
• Preferable start an interactive session or a job.

References

https://s3-us-west-2.amazonaws.com/qiime2-workshops/fmt-cdiff/index.html#fmt-for-recurrent-clostridium-difficile-infection-tutorial

https://isugenomics.github.io/bioinformatics-workbook/dataAnalysis/Metagenomics/Qiime2.html

http://compbio.ucsd.edu/wp-content/uploads/2018/07/20180621_oslo_university_microbiome_analysis_with_qiime2_tutorial.pdf

https://chmi-sops.github.io/mydoc_qiime2.html

https://forum.qiime2.org/t/q2-phylogeny-community-tutorial/4455