INNUENDO Summer Course

”Genomics in foodborne pathogen surveillance and outbreak investigation”

University of the Basque Country, UPV/EHU, Vitoria-Gasteiz, Basque Country, Spain

 

Day 1. The theory – 12th July 2017

Grade Hall, Las Nieves building, Campus of Araba, UPV/EHU


8.15 Registration and coffee

08.40 – 09.00

Opening of the course, welcome

Javier Garaizar and Institutional Representatives

09.00 – 09.45

WGS in surveillance and outbreak detection of foodborne pathogens

Eduardo Taboada

09.45 – 10.30

WGS and antibiotic resistance

Martin Cormican

10.30 – 11.00

Coffee break

 

11.00 – 11.10

EU Capacity-building projects: INNUENDO

Mirko Rossi

11.10 – 11.30

EU Capacity-building projects: ENGAGE&COMPARE

Valeria Bortolaia

11.30 – 12.00

From reads to profiles to trees: challenges and solutions in high throughput sequencing data analysis

João Carriço

12.00 – 12.30

Phenotypic prediction using WGS data: virulome and resistome

Valeria Bortolaia

12.30 – 13.30

Lunch

 

13.30 – 13.50

QA/QC and automatization of whole genome sequence analysis: theory

Mirko Rossi

13.30 – 14.10

QA/QC and automatization of whole genome sequence analysis: Implementation

Miguel Machado

14.10 – 14.40

GScompare: fast clustering of assembled genomes

Joseba Bikandi

14.40 – 15.00

Whole genome MLST: theory

João Carriço

15.00 – 15.15

Whole genome MLST: implementation

Mickael Silva

15.15 – 15.30

Whole genome MLST: phylogenetic inference and metadata visualization

Bruno Gonçalves

15.30 – 16.00

Coffee break

 

16.00 – 16.30

A road map to national WGS based surveillance of foodborne bacteria, Finland

Saara Salmenlinna

16.30 – 17.00

Standardized communication during outbreak investigation

Mirko Rossi




























































17.00 Remarks and closing of the day

19.00 Venue and Social event



Day 2. The practice – 13th July 2017

Informatics room, Las Nieves building, Campus of Araba, UPV/EHU

 

08.40 – 09.00

Content of the day, division of groups, setting computer environment

Joseba Bikandi

09.00 – 09.20

Overview of the INNUENDO platform and its modules

João Carriço

09.20 – 09.45

The INNUENDO platform: the user interface

Bruno Gonçalves

09.45 – 10.45

The INNUENDO platform: QA/QC analysis – INNUca (Part 1)

Miguel Machado

10.45 – 11.15

Coffee break

 

11.15 – 12.15

The INNUENDO platform: QA/QC analysis – INNUca (Part 2)

Miguel Machado

12.15 – 12.45

The INNUENDO platform: GScompare for species determination

Joseba Bikandi

12.45 – 14.00

Lunch

 

14.00 – 15.30

The INNUENDO platform: cg/wgMLST using chewBACCA

Mickael Silva

15.30 – 16.15

The INNUENDO platform: from analysis to action, interpreting trees

Bruno Gonçalves

16.15 – 18.00

Working in groups, self-learning/testing – Free Coffee break

Miguel Machado

Mickael Silva

Bruno Gonçalves























19.00 Social event

Ċ
Javier Garaizar Candina,
Feb 8, 2017, 4:13 AM
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