Live Long Read Sequencing and Data Analysis

15-17 May 2019

Laurent Falquet

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

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

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.

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 

lunch 

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

lunch 

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) 

lunch 

13:30 Finishing exercises

15:00 wrap-up & farewell

Bern and Fribourg (15.5.: seminar room IFIK, Friedbühlstrasse 51, Bern / 16-17.5.: room 2.223 of PER14, Fribourg)

Please note that the course will happen in 2 different locations:

a) at IFIK in Bern (Wednesday): seminar room IFIK, Friedbühlstrasse 51 (take bus Nr 11 to Holligen)

b) at UniFr (Thursday and Friday): room 2.223 of PER14 (take bus Nr 1,3, 7 or 9 to Charmettes)

We will start the lectures at 9:15am and end at 5pm.

Requirements: a laptop with a terminal application (Linux or MacOSX) with eduroam capable wifi access..Windows users should install a free terminal application (e.g., Putty).

Optional: installation of MAUVE software (http://darlinglab.org/mauve/download.html) Warning only compatible with Java 8 (not above).

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.

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