Long reads applied to plant genome assembling
13 June 2018
For-profit: 0 CHF
No future instance of this course is planned yet
This course is co-organised by the CUSO/StarOmics doctoral program. Priority is given to its members, but is open to everyone.
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.
Audience
This course is addressed in priority to PhD students and postodcs.
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
*Technical
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.
Application
Registration is open, please click this link.
No registration fees for members of staromics, otherwise they are 120 CHF for academics and non-profit organizations. This includes course content material and coffee breaks. Participants from for-profit institutions should contact us before application.
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 our general conditions.
You will be informed by email of your registration confirmation.
Venue and Time
University of Lausanne, Génopode building, classroom 2020 (Metro M1 line, Sorge station).
The course will start at 8:30 and end around 17:00.
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 - 010.00 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
Additional information
Coordination: Corinne Dentan (CUSO/Staromics), Grégoire Rossier (SIB)
You are welcome to register to the SIB courses mailing list to be informed of all future courses and workshops, as well as all important deadlines using the form here.
For more information, please contact training@sib.swiss.