Location & dates EMBL Heidelberg, Germany 12 - 15 Jun 2018
Deadlines Application closed
organiser_Nanopore

EMBL Courses and Conferences during the Coronavirus pandemic

With the onsite programme paused, many of our events are now being offered in virtual formats.


Registration is open as usual for many events, with back-up plans in place to move further courses and conferences online as necessary. Registration fees for any events affected by the COVID-19 disruption are fully refundable.


More information for participants of events at EMBL Heidelberg can be found here.

Programme

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Day 1 - Tuesday 12 June 2018
TimeSpeakerLocation
09:00

Self-introduction, project presentation
(2 slides from each participant 5 min)

Flex Lab A+B
Introduction to Nanopore Sequencing
Flex Lab A+B

Coffee break

Flex Lab A+B

Sample and library prep theory

Flex Lab A+B

Introduction to phylogenetics/species identification

Flex Lab A+B

Lunch

EMBL Canteen
Afternoon

QC DNA samples

Training Lab B

Set up 16S PCR

Training Lab B

Introduction to MinKNOW and QC flow cells

Training Lab B 

Coffee Break

Flex Lab A+B

Optional: Q&A session on command line and Linux

Computer Training Lab

18.00

Guided tour

19.00

Course Dinner Downtown at Restaurant Goldener Falke

Day 2 - Wednesday 13 June 2018
TimeSpeakerLocation
09:00

Flow-cell priming and library loading

Flex Lab A+B

Library prep for 16S
(2 flow cells, 12 barcodes per flow cell)

Training Lab B

Library prep for 1D
(2 flow cells – 6 barcodes per flow cell)

Training Lab B

Coffee Break

Computer Training Lab

Flow-cell loading practice and library loading

Training Lab B

Lunch

EMBL Canteen

Afternoon

Assessing a GridION/MinION run

Training Lab B

Introduction to Dogfish/basecalling

Introduction to Epi2ME/16S workflow/WIMP

Computer Training Lab

Coffee break

Computer Training Lab

Set up 16S/WIMP workflows

Computer Training Lab

Optional: Q&A session on command line and Linux

Computer Training Lab

Dinner

EMBL Canteen

Day 3 - Thursday 14 June 2018
TimeSpeakerLocation
09:00

Library prep for rapid barcoding E.Coli
(2 flow cells - 12 barcodes per flow cell)

Training Lab B

Flow-cell loading practice and library loading

Training Lab B

Coffee Break

Computer Training Lab

Assessing a GridION/MinION run

Training Lab B

Lunch

EMBL Canteen

Afternoon

Data Analysis
Introduction of analysis tools used in day 4

Computer Training Lab

Using the Oxford Nanopore technology for de-novo plant genome sequencing
Maximilian Schmidt, RWTH Aachen University, Germany

Computer Training Lab

Coffee Break

Computer Training Lab

Run through an example data set
(E.coli and direct RNA)

Computer Training Lab

Dinner

EMBL Canteen

Day 4 - Friday 15 June 2018
TimeSpeakerLocation
09:00

Review runs

Training Lab B

Review 16S/WIMP workflows

Computer Training Lab

Coffee Break 

Computer Training Lab

Data Analysis (follow data analysis script on chosen datasets)
Basecalling with Albacore
Exploring read length & quality score distribution
Mapping the filtered data to a reference
Visualizing the alignment using Tablet

De novo assembly with Miniasm and Racon
Determining Assembly quality
Assembly polishing with Nanopolish
Methylation detection with Nanopolish

Computer Training Lab

Lunch  

EMBL Canteen
Afternoon

Data Analysis continued


Computer Training Lab

Group presentation with data analysis results
(3-4 slide per group/10 min)

Flex Lab A+B
15:15

End of the course and bus departure