Metagenomics Taxonomic Classification Using Kraken 2 in OmicsBox

Explore metagenomics analysis and taxonomic classification using Kraken 2 in BioBam's OmicsBox tool in this 42-minute video tutorial. Learn about targeted sequencing and shotgun WGS approaches, metagenomics workflows, and research applications. Follow a case study demonstrating study design and practical analysis steps. Witness quality control, pre-processing, taxonomic classification, and output interpretation on the OmicsBox platform. Gain insights into FastQC reports, read trimming with Trimmomatic, Kraken 2 classification, and visualization techniques like Krona charts, principle coordinate analysis, and stacked bar charts. Conclude with an overview of differential abundance analysis for taxa.

Intro
Metagenomics approaches
Overview of metagenomics workflow steps
Questions metagenomics analysis help to answer?
Case study and study design
About BioBam
Exploring OmicsBox
Downloading metagenomics data
Performing QC on raw reads using FastQC
Assessing FastQC report in OmicsBox
QC Fail: Per Sequence GC Content
QC Fail: Per Base Sequence Content
Trimming reads using Trimmomatic
Assessing Trimmomatic report in OmicsBox
Post-trimming QC
Performing Taxonomic classification using Kraken 2
Exploring Kraken 2 report
Krona Charts to visualize taxonomic classification
Principle Coordinate Analysis
Stacked bar charts to visualize relative abundances of taxa
Differential Abundance Analysis of taxa