NGS module

Responsible
Carla Mavian and Matia Prosperi

TIME

CONTENT

SPEAKERS

SUNDAY X AUGUST

17:00
to
18:00

Welcome to VEME

TBA

18:00
to
20:00

Coffee break.

Monday X AUGUST

07:00
to
08:00

Registration.

8:00
to
8:30

Welcome and practical instructions

TBA

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 X 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 X 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.

17:00
to
17:30

Keynote 1:

TBA

17:30
to
18:00

Keynote 2:

TBA

Thursday X 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