Long reads applied to plant genome assembling

20 - 21 June 2018

Ioannis Xenarios

SIB Training Group, Dr. Grégoire Rossier

Dr. Sergey Koren (NHGRI), Dr. Emanuel Schmid (Vital-IT/SIB), Prof. Robert Waterhouse (DEE/UNIL/SIB), Dr. Damien Lieberherr (Swiss-Prot/SIB)

Overview

The aim of this course is to familiarise the participants with long read (also called "third generation") sequencing technologies, their applications and the bioinformatics tools used to assemble this kind of data. Multiple sequencing platforms, including Pacific Biosciences and Oxford Nanopore MinION, are now available to generate reads that are several kilobases-long. This will be demonstrated on a non-model organism such as oak genome that has been studied at the University of Lausanne (www.napoleome.ch). Participants will assemble a plant genome during hands-on sessions, which will serve as an exemplar how to tackle genome assembly and all the assessment that are necessary in today's research.

This course will be composed of an introduction to the techniques and data analysis methods, a minisymposium and a hands-on session. The minisymposium will consist of short presentations by researchers on the applications of these technologies and algorithm behind fast and accurate assembly. The mini symposium will host a scientist from the NHGRI (Sergey Koren), Emmanuel Schmid (Vital-IT/SIB), Robert Waterhouse (DEE/UNIL/SIB), Damien Lieberherr (Swss-Prot/SIB). The speakers will cover topics from genome assembly to evaluation of annotation and gene correction.

Learning objectives

At the end of the course, the participants are expected to have learned what is the current state of the art technology and approaches and caveat in genome assembly assessment.

Prerequisites

You are required to bring your own laptop. We will work on the Vital-IT cluster and we will provide a temporary account for participants who are not users of this cluster.

Programme

1st day: Assembly of long reads

08.30 - 08.45 Welcoming

08.45 - 09.15 Philippe Reymond: Assembly of the Oak genome and assessment of somatic mutations

09.15 - 09.45 Emanuel Schmid: overview on single molecule sequencing and assembly of long reads

09.45 - 10.00 Coffee break

10.00 - 10.30 Sergey Koren: presentation of the assembler Canu and latest developments

10.30 - 11.30 Demo of Sergey Koren, assembly of E. coli

11.30 - 12.30 Lunch break

12.30 - 15.00 Hands-on: assembling in small groups a plant contig

15.00 - 15.15 Coffee break

15.15 - 17.00 Hands-on: continuing genome assembly

2nd day: Evaluation of genome assemblies

08.30 - 08.45 Welcoming

08.45 - 09.15 Robert Waterhouse: BUSCO- assessing genome assembly and annotation completeness

09.15 - 09.45 Damien Liebherr: SwissProt and the curation of (plant) proteins

09.45 - 10.00 Coffee break

10.00 - 10.30 Emanuel Schmid: comparison and evaluation of genome assemblies

10.30 - 12.00 Hands-on: comparison of assembled genomes (& to reference)

12.00 - 13.00 Lunch break

13.00 - 15.00 Hands-on: comparison of assembled genomes

15.00 - 15.15 Coffee break

15.15 - 17.00 Hands-on: gene prediction

University of Lausanne, Génopode building, classroom 2020 (Metro M1 line, Sorge station)

This course is free to CUSO PhD students. Participants who are not CUSO PhD students and/or from non-academic institutions will be charged CHF 120.-.

Deadline for registration and free-of-charge cancellation is set is set to 13/06/2018. Cancellation after this date will not be reimbursed. Please note that participation to SIB courses is subject to general conditions.

You will be informed by email of your registration confirmation.

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