VEME2022 – NGS module

Responsible
Matia Prosperi and Carla Mavian

TIME

CONTENT

SPEAKERS

SUNDAY 21 AUGUST

14:00
to
16:00

Registration.

16:00
to
16:40

Welcome to VEME.

Jairo Mendez, Luiz Alcantara, Tulio de Oliveira, Juan Miguel Pascale, Ana Riviere, Luis Sucre

16:40
to
17:00

Keynote lecture 1: Genomic pathogen surveillance in Panama, from research to public health, Gorgas Memorial Institute experience

Alexander Martinez

17:00
to
17:20

Keynote lecture 2: PAHO Genomic Surveillance Regional Networks: genomics to support public health response for the world

Juliana Leite

17:20
to
17:30

Questions & Answers

A. Martinez​ and J. Leite

17:30
to
19:00

Keynote lecture 3: Collaboration in South Africa to help the world on the characterisation of pandemics and epidemics

Tulio Oliveira

19:00
to
21:30

VEME Cocktail​

Monday 22 AUGUST

8:30
to
9:00

Welcome and practical instructions.

L Franco and L. Alcantara

9:00
to
10:30

Introduction to next generation sequencing.

R. Scheuermann

10:30
to
11:00

Coffee break.

11:00
to
12:30

Introduction to NGS software.

R. Torrieri

12:30
to
14:00

Lunch.

14:00
to
15:00

Reference alignment and SNP calling.

C. Mavian, T. Paisie, M. Tagliamonte

15:00
to
16:00

Software practice for reference alignment and SNP calling.

C. Mavian, T. Paisie., M. Tagliamonte

16:00
to
17:00

Coffee break + poster session.

17:00
to
17:40

Keynote lecture 4: A transdisciplinary approach to pandemic preparedness

A-M Vandamme

17:40
to
18:20

Keynote lecture 5: Portable DNA sequencing: impacting the response to emerging and re-emerging viral pathogens on the ground

M. Giovanetti

Tuesday 23 AUGUST

8:30
to
9:30

De novo assembly.

H. Schmidt

9:30
to
10:30

Bacterial and Viral Bioinformatics Resource Center (BV-BRC).

R. Scheuermann.

10:30
to
11:00

Coffee break.

11:00
to
12:30

Nanopore-based sequencing for routine genomics surveillance

JE. San, V. Fonseca, H. Tegally

12:30
to
13:30

Lunch.

13:30
to
14:30

Nanopore-based sequencing for routine genomics surveillance

JE. San, V. Fonseca, H. Tegally

14:30
to
15:30

Software practice for de novo assembly.

Y. Zhang, T. Paisie, M. Tagliamonte

15:30
to
16:00

Coffee break.

16:00
to
16:50

Free computer time.

Y. Zhang, T. Paisie, M. Tagliamonte, R Kato, L Paixao and S Ortiz.

16:50
to
17:10

Keynote lecture 7: Project VigenDA: Genomic Surveillance of Dengue in the Americas​​.

Jorge L. Munoz

17:10
to
18:10

Keynote lecture 8: Putting ecology into virus evolution​​.

Edward Holmes

Wednesday 24 AUGUST

8:00
to
8:30

Keynote lecture 9: Modernizing Pathogen Surveillance with Fully Automated Genomic Sequencing and Data Ecosystem​​

Sasan Amini

8:30
to
9:30

Transcriptomics, RNASeq, scRNAseq.

R. Scheuermann

9:30
to
10:30

SARS-CoV-2 sequence analysis and mutation profiling with Genomedetective

H. Tegally, JE. San, K. Deforche, V. Fonseca

10:30
to
11:00

Coffee break.

11:00
to
12:30

Keynote lecture NGS: Rapid, Fully Automated Genomic Surveillance Platform, for Actionable Insights for Public Health Laboratories

Sasan Amini

12:30
to
13:30

Lunch.

13:30
to
14:30

Software practice for transcriptomics, RNASeq

R. Scheuermann, Y. Zhang

14:30
to
16:00

Free computer time

R. Scheuermann, Y. Zhang, R Kato, L Paixao and S Ortiz.

16:00
to
17:00

Coffee break + poster session.

17:00
to
17:40

Keynote lecture 10: Quick and Accurate identification of SARS-CoV-2 Variants and Lineages in Africa

H Tegally

17:40
to
18:20

Keynote lecture 11: Modeling and forecasting virus evolution and pathogenesis in the XXI century: from genomic epidemiology to single cell sequencing

M Salemi

Thursday 25 August

8:00
to
8:30

Keynote lecture 6: Molecular Epidemiology based on Ampliseq Technology: SARS-CoV 2 and Beyond.

Gonzalo Sepulveda

8:30
to
9:30

Metagenomics

H. Schmidt.

9:30
to
10:30

Antimicrobial Resistance - AMR

S. Marini

10:30
to
11:00

Coffee break.

11:00
to
12:30

Galaxy for HIV

S. Pond

12:30
to
13:30

Lunch.

13:30
to
14:30

Software practice for metagenomics

C. Mavian, H. Schmidt, M. Tagliamonte

14:30
to
15:30

Free computer time.

C. Mavian, H. Schmidt, M. Tagliamonte, R Kato, L Paixao and S Ortiz.

15:30
to
16:00

Coffee break.

16:00
to
17:30

Free computer time.

C. Mavian, M. Tagliamonte, R Kato, L Paixao and S Ortiz.

18:30
to
20:30

Course teachers dinner