Embedded Files
Day 1
23rd January 2023
23rd January 2023
Registration and Welcome
8.00 a.m. – 8.30 a.m.
8.30 a.m.
Opening Ceremony, Pre-workshop evaluation and Pictures
Opening Ceremony, Pre-workshop evaluation and Pictures
[PA/AvT/BA/IDO/BAM]
9.00 a.m.
Special Seminar: History of bacterial genomics
Special Seminar: History of bacterial genomics
[Prof. Julian Parkhill]
Tea/Coffee Break 10 a.m.–10.30 a.m.
10.30 a.m.
Introduction to Whole Genome Sequencing (WGS)
Introduction to Whole Genome Sequencing (WGS)
[PA/AvT]
Lecture: 20 min
Exercise: 10 min
11.00 a.m.
Introduction to UNIX:
Introduction to UNIX:
The Unix Shell
The Unix Shell
[PA/AvT]
Lecture: 10 min
11.10 a.m.
Introduction to UNIX:
Introduction to UNIX:
Navigating Files and Directories
Navigating Files and Directories
[PA/AvT]
Lecture: 40 min
Exercise: 20 min
12.10 p.m.
Introduction to UNIX:
Introduction to UNIX:
Text Manipulation
Text Manipulation
[PA/AvT]
Lecture: 20 min
Exercise: 10 min
12.40 p.m.
Wrap up for morning session
Wrap up for morning session
[PA/AvT]
10 min
12.50 p.m.
Interactive Quiz I
Interactive Quiz I
[PA/AvT]
Quiz: 10 min
Lunch 1.00 p.m. – 2.00 p.m.
2.00 p.m.
Introduction to UNIX:
Introduction to UNIX:
Combining Commands
Combining Commands
[PA/AvT]
Lecture: 20 min
Exercise: 10 min
2.30 p.m.
Introduction to UNIX:
Introduction to UNIX:
Using Remote Resources
Using Remote Resources
[PA/AvT]
Lecture: 20 min
Exercise: 10 min
3.00 p.m.
Introduction to UNIX:
Introduction to UNIX:
Visual Studio Code
Visual Studio Code
[PA/AvT]
Lecture: 20 min
3.20 p.m.
Interactive Quiz II
Interactive Quiz II
[PA/AvT]
Quiz: 10 min
Tea/Coffee Break 3.30 pm. – 4.00 p.m.
4.00 p.m.
Introduction to UNIX:
Introduction to UNIX:
Bonus - Finding Things
Bonus - Finding Things
[PA/AvT]
Lecture: 20 min
Exercise: 10 min
4.30 p.m.
Introduction to UNIX:
Introduction to UNIX:
Bonus - Loops
Bonus - Loops
Bonus - Shell Scripts
Bonus - Shell Scripts
[PA/AvT]
Lecture: 40 min
Exercise: 10 min
5.20 p.m.
Wrap up for day
Wrap up for day
[PA/AvT]
20 min
Day Closed - 5.30 p.m.
Day Closed - 5.30 p.m.
Day 2
24th January 2023
24th January 2023
8.30 a.m.
Recap of Day 1
Recap of Day 1
Participant Representative:
30 min
9.00 a.m.
Common File Formats
Common File Formats
[PA/AvT]
Lecture: 20 min
Exercise: 10 min
9.30 a.m.
Sequencing Quality Control I
Sequencing Quality Control I
[PA/AvT]
Lecture: 20 min
Exercise: 10 min
Tea/Coffee Break 10.00 a.m. – 10.30 a.m.
10.30 a.m.
Sequencing Quality Control II
Sequencing Quality Control II
[PA/AvT]
Lecture: 60 min
Exercise: 30 min
12.00 p.m.
Wrap up for morning session
Wrap up for morning session
[PA/AvT]
20 min
12.20 p.m.
Interactive Quiz III
Interactive Quiz III
[PA/AvT]
Quiz: 10 min
Lunch 12.30 p.m. – 1.30 p.m.
1.30 p.m.
Short Read Mapping I:
Short Read Mapping I:
Mapping to a reference
Mapping to a reference
[PA/AvT]
Lecture: 30 min
Exercise: 20 min
2.20 p.m.
Short Read Mapping II:
Short Read Mapping II:
Genome Visualization
Genome Visualization
[PA/AvT]
Lecture: 30 min
Exercise: 30 min
3.20 p.m.
Interactive Quiz IV
Interactive Quiz IV
[PA/AvT]
Quiz: 10 min
Tea/Coffee Break 3.30 p.m. – 4.00 p.m.
4.00 p.m.
Short Read Mapping III:
Short Read Mapping III:
Variant Calling
Variant Calling
[PA/AvT]
Lecture: 30 min
Exercise: 10 min
4.40 p.m.
Short Read Mapping IV:
Short Read Mapping IV:
Generating a Consensus Sequence
Generating a Consensus Sequence
[PA/AvT]
Lecture: 20 min
Exercise: 10 min
5.10 p.m.
Wrap up for day
Wrap up for day
[PA/AvT]
20 min
Day Closed - 5.30 p.m.
Day Closed - 5.30 p.m.
Day 3
25th January 2023
25th January 2023
8.30 a.m.
Recap of Day 2
Recap of Day 2
Participant Representative:
30 min
9.00 a.m.
Open Lecture
Open Lecture
[....]
9.30 a.m.
Genome Assembly and Annotation I:
Genome Assembly and Annotation I:
de novo assembly with shovill
de novo assembly with shovill
[AvT/PA]
Lecture: 30 min
Exercise: 10 min
Tea/Coffee Break 10.10 a.m. – 10.40 a.m.
10.40 a.m.
Genome Assembly and Annotation II:
Genome Assembly and Annotation II:
Annotation with Bakta
Annotation with Bakta
[AvT/PA]
Lecture: 20 min
Exercise: 10 min
11.10 a.m.
Managing software I:
Managing software I:
Software Managers
Software Managers
[AvT/PA]
Lecture: 30 min
Exercise: 10 min
11.50 a.m.
Managing software II:
Managing software II:
Virtual Environments and Containers
Virtual Environments and Containers
[AvT/PA]
Lecture: 30 min
Exercise: 10 min
12.30 p.m.
Interactive Quiz V
Interactive Quiz V
[AvT/PA]
Quiz: 10 min
Lunch 12.40 p.m. – 1.40 p.m.
1.40 p.m.
Workflow Managers and Pipelines
Workflow Managers and Pipelines
[AvT/PA]
Lecture: 40 min
Exercise: 20 min
2.40 p.m.
Introduction to High Performance Computing (HPC)
Introduction to High Performance Computing (HPC)
[BA/AvT/PA]
Lecture: 20 min
Exercise: 20 min
3.20 p.m.
Interactive Quiz VI
Interactive Quiz VI
[AvT/PA]
Quiz: 10 min
Tea/Coffee Break 3.30 p.m. – 4.00 p.m.
4.00 p.m.
Support to install tools on personal machines
Support to install tools on personal machines
[AvT/PA/BA/IDO/BAM]
5.00 p.m.
Wrap up for day
Wrap up for day
[AvT/PA]
30 min
Day Closed - 5.30 p.m.
Day Closed - 5.30 p.m.
Day 4
26th January 2023
26th January 2023
8.30 a.m.
Recap of Day 3
Recap of Day 3
Participant Representative:
30 min
9.00 a.m.
Bioinformatics pipeline
Bioinformatics pipeline
[Marco van Zwetselaar]
9.30 a.m.
The nf-core pipelines
The nf-core pipelines
[AvT/PA]
Lecture: 45 min
Exercise: 15 min
Tea/Coffee Break 10.30 a.m. – 11.00 a.m.
11.00 a.m.
The nf-core/bactmap pipeline I
The nf-core/bactmap pipeline I
[AvT/PA]
Lecture: 60 min
Exercise: 30 min
12.30 a.m.
Interactive Quiz VII
Interactive Quiz VII
[AvT/PA]
Quiz: 10 min
Lunch 12.40 p.m. – 1.40 p.m.
1.40 p.m.
The nf-core/bactmap pipeline II:
The nf-core/bactmap pipeline II:
Looking at the results
Looking at the results
[AvT/PA]
Lecture: 45 min
Exercise: 15 min
2.40 p.m.
Introduction to phylogenetics I:
Introduction to phylogenetics I:
Multiple sequence alignment and Phylogenetic Tree Inference
Multiple sequence alignment and Phylogenetic Tree Inference
[AvT/PA]
Lecture: 50 min
3.30 p.m.
Interactive Quiz VIII
Interactive Quiz VIII
[AvT/PA]
Quiz: 10 min
Tea/Coffee Break 3.40 p.m. – 4.10 p.m.
4.10 p.m.
Introduction to phylogenetics II:
Introduction to phylogenetics II:
Visualization of Phylogenetic Trees
Visualization of Phylogenetic Trees
[AvT/PA]
Lecture: 40 min
Exercise: 40 min
05.30 p.m.
Wrap up for day
Wrap up for day
[AvT/PA]
10 min
Day Closed - 5.40 p.m.
Day Closed - 5.40 p.m.
Workshop Dinner @ 7.00 p.m.
Workshop Dinner @ 7.00 p.m.
Day 5
27th January 2023
27th January 2023
8.30 a.m.
Recap of Day 4
Recap of Day 4
Participant Representative:
30 min
9.00 a.m.
Genotyping and Antimicrobial Resistance Prediction I
Genotyping and Antimicrobial Resistance Prediction I
[PA/AvT]
Lecture: 60 min
Exercise: 30 min
Tea/Coffee Break 10.30 a.m. – 11.00 a.m.
11.00 a.m.
Genotyping and Antimicrobial Resistance Prediction II
Genotyping and Antimicrobial Resistance Prediction II
[PA/AvT]
Lecture: 30 min
Exercise: 30 min
12.00 p.m.
Support to install tools on personal machines
Support to install tools on personal machines
[AvT/PA/BA/IDO/BAM]
12.40 p.m.
Wrap up for morning session
Wrap up for morning session
[AvT/PA]
10 min
12.50 p.m.
Interactive Quiz IX
Interactive Quiz IX
[PA/AvT]
Quiz: 10 min
Lunch 1.00 p.m. – 2.00 p.m.
2.00 p.m.
Participants Presentations
Participants Presentations
[All Participants]
8 min each
Tea/Coffee Break 4.00 p.m. – 4.30 p.m.
4.30 p.m.
Bringing it all together:
Bringing it all together:
Course wrap up
Course wrap up
[AvT/PA/BA/IDO/BAM]
30 min
5.00 p.m.
Post-Workshop Evaluation and Certification
Post-Workshop Evaluation and Certification
[All Participants]
20 min
Workshop Closure - 5.30 p.m.
Workshop Closure - 5.30 p.m.
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