Viromics Workshop

Welcome to the Virus discovery by metagenomics: assembly, identification, annotation workshop, included in the series of courses by the ITN ViroInf.

Day 1: Re-discovering crAssphages in the original data but with modern tools
Day 2: Comparing metagenomic virus discovery tools using different signals
Day 3: Identifying genes, clustering protein families, and annotating functions
Day 4: Taxonomic classification: gene content clustering and phylogenetic analysis
Day 5: Tracking ecological dynamics using compositional data analysis

Schedule

		Setup	Download files required for the lesson
Day 1	09:00	1. Welcome	Who is sitting next to me? What are we going to do in this workshop?
	10:00	2. Listen to Assembly lecture
	10:45	3. The dataset	What is metagenomics? What do we call viral dark matter? Where does the dataset come from? What format is the sequencing data?
	11:05	4. Metavirome assembly	What is a sequence assembly? How is different a cross-assembly from a normal assembly?
	12:05	5. Lunch break
	13:00	6. Visualizing the assembly graph	How the k-mer size contributes to the conectivity of the graph? Are related species connected in the graph?
	13:50	7. Assessing assemblies quality	Which assembly contains longer contigs? Which assembly best represents the raw data (sequencing reads)?
	14:30	8. Binning contigs	How many bins do we obtain?
	15:45	Finish
Day 2	09:00	9. Setup and run DeepVirFinder	Why do we use different environments for different tools? How do we run DeepVirFinder?
	09:30	10. Listen to Virus Detection lecture
	10:30	11. Setup and run PPR-Meta	How do we install and run PPR-Meta? How are PPR-Meta and DeepVirFinder different?
	11:00	12. Setup and Run VirFinder	How do we run VirFinder and how is it different from the other tools?
	11:30	13. Comparing Virus Identification Tools	How can we compare the results of different virus identification tools? Which tool finds more phages? Why would the tools disagree?
	12:00	14. Setup and run VirSorter	How do we install and run VirSorter? How is VirSorter different than the previous tools?
	12:30	15. Lunch Break	What is the tastiest food we can find in the vicinity?
	13:20	16. Compare Results for four tools	How different are the predictions of the tools per contig? How sensitive are the different tools we used?
	15:20	17. Prophage Prediction	How is prophage prediction similar/different from free virus prediction? How do I find detailed information about my results in several output folders?
	16:00	18. Listen to Benchmarking lecture
	17:00	Finish
Day 3	09:00	19. Introduction and setting up
	09:15	20. Gene prediction
	10:00	21. Prodigal modes
	11:00	22. Functional annotation
	12:00	23. Lunch break
	12:50	24. Clustering proteins
	13:50	25. Integrating annotations
	14:50	26. Inspecting the MSAs
	15:30	Finish
Day 4	09:00	27. Install R package
	09:10	28. Clustering and taxonomic classification of uncultivated viral genomes	What are we going to do today?
	09:25	29. Required data
	09:35	30. Homology based search	If we classify our viral sequences with Blast, in which cases do you expect that blast sequence searches result in good hits? What would you do if your sequence hit different viral (or bacterial) sequences with low coverage of your query sequence, or low sequence identity with the hit?
	10:05	31. Clustering viral sequences based on shared proteins	Can we cluster viral sequences based on shared protein clusters?
	11:05	32. Installing and running Vcontact2	How do we install and run Vcontact2?
	11:35	33. Lunch break
	12:25	34. Check Vcontact2	Did we successfully run Vcontact2?
	12:35	35. Phylogeny based on marker genes	Can we use marker genes to infer phylogeny and taxonomy?
	13:35	36. Gene sharing networks with Vcontact2	Can we assign a genus-level taxonomic annotations with vContact2? Do contigs from the same bin cluster together? How do the vContact2 results compare to other methods we used?
	15:05	37. Assessing viral contigs completeness and contamination	Which signals can we use to assess how complete and/or contaminated is our viral contig?
	15:35	Finish
Day 5	09:00	38. Track alpha and beta diversity dynamics of viral/microbial communities	What is compositional data? How to do compositional data analysis? What is Hill Number?
	11:00	39. Rstudio set up from Conda environment, package installment and data download
	11:30	40. Exploring data	What are the differences between absulte abundance and relative abundance? Why is it necessary to filter out low-abundance features?
	12:30	41. Break
	13:30	42. Alpha diversity	What is alpha diversity? What common alpha diversity indices are there? How to compare alpha diversity between samples?
	15:00	43. Beta diversity	What is beta diversity? How to compare beta diversity between samples?
	15:30	44. Differential abundance	Which features vary in abundance with categorical variables?
	16:00	Finish

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.