Detailed information about the course

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Live Long Read Sequencing and Data Analysis


15-17 May 2019

Lang EN Workshop language is English
Responsable de l'activité

Laurent Falquet


Dr. Laurent Falquet (UniFr) and Dr. Alban Ramette (UniBe)


3 Swiss speakers to be announced


The ability to conduct a sequencing run on its own very small instrument (the size of a hand) like the minION is very tempting for each lab researcher. During this course, we will show how to prepare, run and analyse a DNA sample using a minION. Days description of the preliminary program: 1-am General Intro+DNA library prep (organisers: need a lab with material freezer and centrifuge) 1-pm running minION (organisers: overnight need a computer connected to minION) 2-am data QC and cleaning (FastQC, or other tools) 2-pm genome assembly (Canu or other tools) and polishing 3-am analysis & annotation (Prokka and other tools) 3-pm comparison with PacBio (MAUVE and other tools) The participants will learn the tips and tricks required to prepare their DNA samples, run the sequencer and analyse the data with basic methods. The pitfalls to avoid will also be discussed.


Preliminary program:
DAY1 (IFIK, Bern):
9:15 Introduction to long read sequencing (ONT, PacBio)
10:00 Library prep tour (rapid, 1D, 1D2, 2D)
11:00 Barcoded Library prep with prepared DNA of S.aureus, load minION or GridION 
13:30 examples of long read usage 
15:00 verify sequencing state, demo of the MinKnow interface 

DAY2 (UniFr):
9:15 UNIX reminder
10:00 HPC intro
11:00 Sequencing status (how many reads after ~24h); QC and cleaning, demultiplexing
13:30 Genome assembly with Canu+Pilon, Unicycler or other pipelines 
15:00 Hybrid assembly Illumina+ONT and Spades 

DAY3 (UniFr):
9:15 Sequencing status (How many reads after ~48h); Annotation (prokka)
11:00 Comparative analysis (individual, grouped, long read only vs hybrid, with PacBio) (MAUVE, roary) 
13:30 Finishing exercises
15:00 wrap-up & farewell


Bern and Fribourg


Reimbursements for CUSO StarOmics students

Train ticket, 2°class, half-fare from your institution to the place of the activity.
NO reimbursement for your meal expenses

Reimbursement form attached with original tickets has to be sent to the StarOmics coordinator Corinne Dentan at University of Lausanne, Centre Intégratif de Génomique, Le Génopode, 1015 Lausanne.

For any question concerning reimbursement please contact the CUSO StarOmics coordinator Corinne Dentan.



Deadline for registration 30.04.2019
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