Metagenomic Course and Virus Discovery

Course program

Day	Period	Local	Class	Subject	Teacher
04/04 Tue	8:30-9:00 am	Room: Samuel Pessoa Building: ICB2	-	Welcome and introduction	Bas and Arthur
	9:00-10:15 am	Room: Samuel Pessoa Building: ICB2	Theory	Virus discovery by metagenomics - an introduction Sample collection Identifying viruses Ethical issues	Bas
	10:45-12:00 am	Room: Samuel Pessoa Building: ICB2	Theory	Assembly strategies for genomics and metagenomics DNA sequencing and quality Assembly algorithms Assembly quality assessment	Bas
	2:00-3:45 pm	Room: 5 Building: ICB4	Practice	Metagenome assembly Using SSH e X2Go Quality evaluation and trimming – FastQC, Cutadapt Metagenome assembly – SPAdes, ABYSS Read mapping – Bowtie, BWA Assessing assembly quality – N50, Samtools Data visualization – Tablet or IGV or Artemis	Bas
	4:15-6:00 pm	Room: 5 Building: ICB4	Practice		Bas
05/04 Wed	9:00-10:15 am	Room: Samuel Pessoa Building: ICB2	Theory	Binning genomes from metagenomes Cross-assembly Binning signals Estimating genome completeness Core and flexible genome	Bas
	10:45-12:00 am	Room: Samuel Pessoa Building: ICB2	Theory	Identifying viral sequences in metagenomes Nucleotide usage Gene order and directionality Marker genes and unknownness	Bas
	10:45-12:00 am	Room: Samuel Pessoa Building: ICB2	Theory	Viral profile HMMs as marker genes Specificity of different databases Viral databases of orthologous groups and profile HMMs: vFams, pVOGs, Viral OGs (viral section of eggNOG)	Arthur
	2:00-3:45 pm	Room: 5 Building: ICB4	Practice	Binning metagenomic contigs Cross-assembly – crAss Depth profiles Metagenome binning - Metabat	Bas
	4:15-6:00 pm	Room: 5 Building: ICB4	Practice		Bas
06/04 Thu	9:00-10:15 am	Room: Samuel Pessoa Building: ICB2	Theory	Profile HMMs and viral discovery Limitations of the currently available databases Rational design of profile HMMs	Arthur
	10:45-12:00 am	Room: Samuel Pessoa Building: ICB2	Theory	Seed-driven progressive assembly Using seed sequences for targeted assembly - GenSeed Profile HMMs as seeds for progressive assembly - GenSeed-HMM Progressive assembly x global assembly	Arthur
	2:00-3:45 pm	Room: 5 Building: ICB4	Practice	Seed-driven progressive assembly Genseed-HMM - sequence reconstruction using profile HMMs Case 1 - reconstructing Alpavirinae phage genomes from fecal samples Case 2 - reconstructing DENV and ZIKV genomes from human patient samples	Arthur
	4:15-6:00 pm	Room: 5 Building: ICB4	Practice		Arthur
07/04 Fri	9:00-10:15 am	Room: Samuel Pessoa Building: ICB2	Theory	Functional annotation Basic concepts Automated pipelines for functional annotation	Arthur
	10:45-12:00 am	Room: Samuel Pessoa Building: ICB2	Theory	Towards understanding the function of viruses CRISPRs Homology Co-abundance	Bas
	2:00-3:45 pm	Room: 5 Building: ICB4	Practice	Student's presentations Deyvid Amgarten, Nicholas di Paula, Suzana Ezquina, Gabriel Peixoto Function interpretation Functional annotation – EGene2 CRISPR matching	Bas and Arthur
	4:15-6:00 pm	Room: 5 Building: ICB4	Practice		Bas and Arthur