Curso Metagenômica e Descoberta de Vírus

Programa do curso

Dia	Horário	Local	Aula	Assunto	Docente
04/04 Ter	8:30-9:00 hs	Sala: Samuel Pessoa Edifício: ICB2	-	Boas vindas e introdução ao curso	Bas e Arthur
	9:00-10:15 hs	Sala: Samuel Pessoa Edifício: ICB2	Teórica	Virus discovery by metagenomics - an introduction Sample collection Identifying viruses Ethical issues	Bas
	10:45-12:00 hs	Sala: Samuel Pessoa Edifício: ICB2	Teórica	Assembly strategies for genomics and metagenomics DNA sequencing and quality Assembly algorithms Assembly quality assessment	Bas
	14:00-15:45 hs	Sala: 5 Edifício: ICB4	Prática	Metagenome assembly Usando SSH e X2Go Quality evaluation and trimming – FastQC, Cutadapt Metagenome assembly – SPAdes, ABYSS Read mapping – Bowtie, BWA Assessing assembly quality – N50, Shstools Data visualization – Tablet or IGV or Artemis	Bas
	16:15-18:00 hs	Sala: 5 Edifício: ICB4	Prática		Bas
05/04 Qua	9:00-10:15 hs	Sala: Samuel Pessoa Edifício: ICB2	Teórica	Binning genomes from metagenomes Cross-assembly Binning signals Estimating genome completeness Core and flexible genome	Bas
	10:45-12:00 hs	Sala: Samuel Pessoa Edifício: ICB2	Teórica	Identifying viral sequences in metagenomes Nucleotide usage Gene order and directionality Marker genes and unknownness	Bas
	10:45-12:00 hs	Sala: Samuel Pessoa Edifício: ICB2	Teórica	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
	14:00-15:45 hs	Sala: 5 Edifício: ICB4	Prática	Binning metagenomic contigs Cross-assembly – crAss Depth profiles Metagenome binning - Metabat	Bas
	16:15-18:00 hs	Sala: 5 Edifício: ICB4	Prática		Bas
06/04 Qui	9:00-10:15 hs	Sala: Samuel Pessoa Edifício: ICB2	Teórica	Profile HMMs and viral discovery Limitations of the currently available databases Rational design of profile HMMs	Arthur
	10:45-12:00 hs	Sala: Samuel Pessoa Edifício: ICB2	Teórica	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
	14:00-15:45 hs	Sala: 5 Edifício: ICB4	Prática	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
	16:15-18:00 hs	Sala: 5 Edifício: ICB4	Prática		Arthur
07/04 Sex	9:00-10:15 hs	Sala: Samuel Pessoa Edifício: ICB2	Teórica	Functional annotation Basic concepts Automated pipelines for functional annotation	Arthur
	10:45-12:00 hs	Sala: Samuel Pessoa Edifício: ICB2	Teórica	Towards understanding the function of viruses CRISPRs Homology Co-abundance	Bas
	14:00-15:45 hs	Sala: 5 Edifício: ICB4	Prática	Apresentações dos estudantes Deyvid Amgarten, Nicholas di Paula, Suzana Ezquina, Gabriel Peixoto Function interpretation Functional annotation – EGene2 CRISPR matching	Bas e Arthur
	16:15-18:00 hs	Sala: 5 Edifício: ICB4	Prática		Bas e Arthur