In this session we will use a set of reads enriched for viral sequences and sequences from wastewater treatment plants. Specifically the aim is to assemble whole SARS-CoV-2 genomes from such samples and to perform whole genome alignments of such assemblies against reference sequence with automatic transfer of annotations. Further, statistical analysis of metagenomic data will be covered to compare groups of samples. All analysis will be carried out using QIAGEN CLC Genomics Workbench Premium.

Learning Objectives:

1. Discuss targeted viral profiling from a metagenomics sample extracted from wastewater.

2. Discuss reference based assembly from metagenomic reads and whole genome alignments.

3. Discuss statistical analysis of metagenomic profiles.