METAGENOMICS DATA ANLAYSIS

Questions

• What is the effect of normal variation in the gut microbiome on host health?

Objectives

• Analyze 16S rRNA sequencing data using Mothur tool suite in Galaxy

• Visualize the composition of the microbial community using Krona and Phinch

• Perform Diversity Analysis & Principal Coordinates Analysis using Mian

In this module, we will cover:

1. Create a free account at usegalaxy.org and login to Galaxy

2. Obtain and prepare 16s rRNA sequencing data

   1. Understand our input data

   2. Import the data into Galaxy

3. Data Quality Control

   1. Create contigs from paired-end reads

   2. Data Cleaning

   3. Optimize files for computation

4. Sequence Alignment

   1. Sequence alignment to reference

   2. Post-alignment Data Cleaning

   3. Chimera Removal

5. Taxonomic Classification

   1. Removal of non-bacterial sequences

6. OTU Clustering

7. Visualizations

   1. Krona

   2. Phinch

8. Diversity Analysis & Principal Coordinates Analysis (PCoA)

   1. Mian

Extra

Working with NCBI SRA single-end data