session timings - Dec 2023 workshop - Githubissues

cambiotraining / bacterial-genomics

Course materials for "Working with Bacterial Genomes"

https://cambiotraining.github.io/bacterial-genomics/

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session timings - Dec 2023 workshop #23

Closed tavareshugo closed 4 months ago

tavareshugo commented 11 months ago

Keeping track of timings for the sessions on the workshop that ran 11th Dec 2023. To help with timetable in the future.

day 1

09:40 - 09:50 Welcome (hugo)
09:50 - 10:15 Know your bug (Andries)
10:15 - 10:45 NGS (Bajuna)
10:45 - 11:00 Workflow managers (Andries)
11:00 - 11:20 break
11:20 - 11:40 Intro to TB (Andries)
11:40 - 12:25 Intro to QC and bacQC (Bajuna)
12:25 - 13:00 Practical
13:00 - 14:00 Lunch
14:00 - 14:30 Practical + solutions
14:30 - 15:10 Mapping (Joana)
15:10 - 15:30 Practical
15:30 - 15:45 Break
15:45 - 16:45 Invited talk
16:45 - 17:00 Wrap-up (Andries)

tavareshugo commented 11 months ago

day 2

09:30 - 09:40 Welcome and recap (Andries)
09:40 - 10:05 Phylogeny (Zachary)
10:05 - 11:00 Practical
11:15 - 11:20 TB-Profiler brief intro (Zachary)
11:20 - 11:50 Practical
11:55 - 12:25 Microreact including live demo (Seb)
12:25 - 12:45 Practical
12:45 - 13:45 Lunch
13:50 - 15:10 Group exercise (Andries)
15:10 - 15:25 break
15:25 - 16:30 Transmission analysis, including practical (Andries)

tavareshugo commented 11 months ago

day 3

09:40 - 10:00 Intro to Staph (Andries)
10:00 - 10:30 Assembly and annotation - up to assembly quality (Antony)
10:30 - 11:30 Guest lecture
11:30 - 11:40 break
11:40 - 11:50 finish assemble quality and assembleBAC pipeline (Antony)
11:50 - 12:45 practical - several people finished earlier
12:45 - 13:45 lunch
14:00 - 14:30 Panaroo (Chris)
14:30 - 14:35 Pathogenwatch demo (Andries)
14:35 - 16:00 Practicals including Panaroo, staph phylogeny, pathogenwatch, microreact (which was scheduled for day 4) (Chris)
Finished at 16:00 (some people still finishing exercise until 16:30)

tavareshugo commented 11 months ago

day 4

09:40 - 10:00 Intro to pneumo (Andries)
10:00 - 10:40 Practical (everyone finished quickly)
10:40 - 11:15 Improvised introduction to fetchngs workflow (Andries)
11:15 - 11:30 break
11:30 - 12:30 Guest lecture
12:30 - 13:30 lunch
13:40 - 14:?? Recombination (Antony)
14:?? - 15:15 Practical
15:15 - 15:30 break
15:30 - 16:00 Mutational signatures (Chris)
16:00 - 16:10 Wrap-up

tavareshugo commented 11 months ago

day 5

09:30 - 09:40 Recap
09:40 - ??:?? AMR (Seb)
??:?? - 11:15 Practical, including pathogenwatch
11:10 - 11:15 Discussion of AMR results of different tools
11:15 - 11:30 break
11:30 - 12:30 Guest speaker
12:30 - 13:30 Lunch
13:30 - 15:15 Bonus exercise (Vibrio)
15:15 - 15:30 break
15:30 - 16:00 Prepare presentations
16:00 - 16:30 Group presentations