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Setup
Episodes
Welcome
Listen to Assembly lecture
The dataset
Metavirome assembly
Lunch break
Visualizing the assembly graph
Assessing assemblies quality
Binning contigs
Setup and run DeepVirFinder
Listen to Virus Detection lecture
Setup and run PPR-Meta
Setup and Run VirFinder
Comparing Virus Identification Tools
Setup and run VirSorter
Lunch Break
Compare Results for four tools
Prophage Prediction
Listen to Benchmarking lecture
Introduction and setting up
Gene prediction
Prodigal modes
Functional annotation
Lunch break
Clustering proteins
Integrating annotations
Inspecting the MSAs
Install R package
Clustering and taxonomic classification of uncultivated viral genomes
Required data
Homology based search
Clustering viral sequences based on shared proteins
Installing and running Vcontact2
Lunch break
Check Vcontact2
Phylogeny based on marker genes
Gene sharing networks with Vcontact2
Assessing viral contigs completeness and contamination
Track alpha and beta diversity dynamics of viral/microbial communities
Rstudio set up from Conda environment, package installment and data download
Exploring data
Break
Alpha diversity
Beta diversity
Differential abundance
Bia Introduction
All in one page (Beta)
Extras
Reference
About
Discussion
Figures
Instructor Notes
License
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Overview
Teaching:
60 min
Exercises:
0 min
Questions
Objectives
Key Points
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