Genome Assembly

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Genome Assembly

 20 - 21  April 2023
13 - 14 October 2022
Wageningen University - Campus

 

 

Scope

This two-day workshop is aimed at providing a basic understanding of creating and evaluating de novo assembly using long read technologies. The workshop requires knowledge of working with the Linux operating system and of biological topics such as genetics and DNA. Although the data is from a plant genome, the learned principles can be applied to many other organisms, including bacteria, fungi and mammals. The idea behind this workshop is that you learn the most by doing and discussing the results.

Topics
- Read Quality assessment. Using bioinformatics tools to check the quality of the reads.
- De novo assembly. Producing genome assemblies based on PacBio, Nanopore and Illumina.
- Assembly comparison. The genome assemblies based on the different types of data might have different results. Here we will compare the results and investigate the found differences between them.
- Assembly base Quality check using mRNA sequence. We will use our NGS data and mRNA sequences to identify SNPs and other discrepancies between the assemblies. We will study the effects these assembly errors have on downstream analyzes.

Programme (tentative)

Day 1:
Morning: Quality control and evaluation of long read data
Afternoon: Assembly of long reads

Day 2:
Morning: Comparison and visualization of long read assemblies
Afternoon: Validation of assemblies

General information
Target Group The workshop is intended for bioinformaticians or researchers who want to learn about application of latest sequencing technologies in genomics.
Group Size Min. 20 / Max. 24 participants
Course duration 2 days
Language of instruction English
Frequency of recurrence At least every 2 years
Number of credits 0.6 ECTS
Lecturers Dr. Sven Warris (Business Unit Bioscience, Wageningen Plant Research, Wageningen University & Research),
Christina Papastolopoulou (DLO HBO Onderzoeker, Wageningen University & Research)
Prior knowledge No prior experience with PacBio or ONT sequencing data is required.
Location Wageningen University Campus, specific location to be announced. Please note that you have to bring your own laptop.
Options for accommodation Accommodation is not included in the fee of the course, but there are several possibilities in Wageningen. For non-WUR PE&RC members 50% of the accommodation costs can be reimbursed with a maximum of €30,- per night. For more information contact Miriam van Heist (miriam.vanheist@wur.nl). For information on B&B's and hotels in Wageningen please visit proefwageningen.nl. Another option is Short Stay Wageningen. Furthermore Airbnb offers several rooms in the area. Finally, there are a number of groups on Facebook where students announce subrent possibilities and things like that. Examples include: Wageningen Room Subrent, Wageningen Room Sublets, and Wageningen Student Plaza. Wageningen has a range of restaurants, but there are also options to have dinner on the University Campus.
Fees 1
  EARLY-BIRD FEE 2 REGULAR FEE 2
PE&RC / WIMEK / WASS / EPS / VLAG / WIAS PhD candidates with an approved TSP € 120,- € 170,-
PE&RC postdocs and staff  € 240,- € 290,-
All other academic participants € 280,- € 330,-
Non academic participants € 500,- € 550,-

1 The course fee includes a reader, coffee/tea, and lunches. It does not include accommodation (NB: options for accommodation are given above)
2 The Early-Bird Fee applies to anyone who REGISTERS ON OR BEFORE 20 February 2023

Note:

  • If you need an invoice to complete your payment, please send an email to office.pe@wur.nl, including ALL relevant details that should be mentioned on the invoice (e.g., purchase order no., specific addresses, attendees, etc.).
  • The Early-Bird policy is such that the moment of REGISTRATION (and not payment) is leading for determining the fee that applies to you.
  • Please make sure that your payment is arranged within two weeks after your registration.
  • It is the participant's responsibility to make sure that he/she (or his/her secretary) completes the payment correctly and in time.
PE&RC Cancellation Conditions
  • Up to 4 (four) weeks prior to the start of the course, cancellation is free of charge.
  • Up to 2 (two) weeks prior to the start of the course, a fee of € 120,- will be charged.
  • In case of cancellation within two weeks prior to the start of the course, a fee of € 280,- will be charged.
  • If you do not show at all, a fee of € 500,- will nevertheless be charged.

Note: If you would like to cancel your registration, ALWAYS inform us and do not assume that by NOT paying the participation fee, your registration is automatically cancelled, because it isn't (and do note that you will be kept to the cancellation conditions).

More information

Dr. Sven Warris
Email: sven.warris@wur.nl

Miriam van Heist (PE&RC)
Email: miriam.vanheist@wur.nl

Registration

To register, please enter your details below and click "Register".