NGS module

Responsible
Carla Mavian and Matia Prosperi

TIME

CONTENT

SPEAKERS

SUNDAY 4 AUGUST

17:00
to
17:50

Welcome to VEME

Luiz Alcantara

17:50
to
18:10

Keynote 1:

Jairo Mendez Rico

18:10
to
18:30

Keynote 2:

Tulio de Oliveira

18:30
to
20:00

Coffee break.

Monday 5 AUGUST

07:00
to
08:00

Registration.

8:00
to
8:30

Welcome and practical instructions

Luiz Alcantara, Marta Giovanetti and Vagner Fonseca​

8:30
to
9:00

Introduction to next generation sequencing

R. Scheuermann

9:00
to
10:00

Reference alignment: theory

C. Mavian

10:00
to
10:30

Coffee break.

10:30
to
12:00

Introduction and logging in to Terra Reference alignment and SNP calling practice (Terra)

C. Tomkins-Tinch, G. Mboowa

12:00
to
13:00

Lunch.

13:00
to
14:30

Reference alignment and SNP calling practice (CMD)

T. Paisie, C. Mavian

14:30
to
15:30

Reference alignment: examining results

T. Paisie, C. Mavian, C. Tomkins-Tinch, G. Mboowa

15:30
to
17:00

Coffee break + poster session.

Tuesday 6 AUGUST

8:00
to
9:00

De novo assembly: theory

H. Schmidt

9:00
to
10:00

De novo assembly practice (Terra & miniWDL)

C. Tomkins-Tinch, G. Mboowa

10:00
to
10:30

Coffee break.

10:30
to
12:00

De novo assembly practice (CMD)

T. Paisie, C. Mavian

12:00
to
13:00

Lunch.

13:00
to
14:30

De novo assembly: examining results

T. Paisie, C. Mavian, C. Tomkins-Tinch, G. Mboowa

14:30
to
15:30

Introduction to computing

C. Tomkins-Tinch

15:30
to
16:00

Coffee break.

16:00
to
17:00

Metagenomics: taxonomic classification with kraken (Terra)

C. Tomkins-Tinch, G. Mboowa

Wednesday 7 AUGUST

8:00
to
9:00

Metagenomics: theory

C. Mavian

9:00
to
10:00

Metagenomics: taxonomy classification with kraken (CMD)

C.Mavian, T. Paisie, Ortiz S

10:00
to
10:30

Coffee break.

10:30
to
12:00

Metagenomics: de novo assembly and blast

Ortiz S, C. Mavian

12:00
to
13:00

Lunch.

13:00
to
14:00

Metagenomics: examining results

C. Tomkins-Tinch, G. Mboowa, C. Mavian, Ortiz S

14:00
to
14:30

Illumina Innovations for Viral Genomics

Leandro Ucela Alves

14:30
to
15:00

Genome detective

K Deforche, V. Fonseca, J. Xavier

15:00
to
16:00

Dashboard

J. Xavier, C.Mavian, T. Paisie

16:00
to
17:00

Coffee break + poster session.

Hybrid Session: https://us06web.zoom.us/j/82087200228?pwd=WjRWKavQ064wYfYQ0ZeaFk9U3I1kGY.1

17:00
to
17:30

Keynote 3: Rapid spatial Expansion Beyond the Amazon Basin: Oropouche Virus joins other main arboviruses in epidemic activity across the Americas

Marta Giovanetti

17:30
to
18:00

Keynote 4: 13 years of genomic surveillance in Haiti

Carla Mavian

18:00
to
18:30

Keynote 5: Mass Dengue Vaccination Campaign in Dourados: A Vaccine Breakthough Case Following Tetravalent Anti-dengue Vaccination

Julio Croda

Thursday 8 August

8:00
to
9:00

Bulk transcriptomics: Theory

R. Scheuermann

9:00
to
10:00

Bulk transcriptomics: Practice 1

R. Scheuermann, D.Pintard

10:00
to
10:30

Coffee break.

10:30
to
12:00

Bulk transcriptomics: Practice 2

R. Scheuermann, D.Pintard

12:00
to
13:00

Lunch.

13:00
to
14:30

Single cell transcriptomics: Theory

R. Scheuermann

14:30
to
15:30

Single cell transcriptomics: Practice 1

D.Pintard, R. Scheuermann, J. Xavier

15:30
to
16:00

Coffee break.

16:00
to
17:30

Single cell transcriptomics: Practice 2

D.Pintard, R. Scheuermann, J. Xavier

18:30
to
20:30

Course teachers dinner