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de novo Assembly from NGS data

general information

  • Next occasion: early 2014
  • Location: Wageningen, The Netherlands
  • Organiser: WUR, LUMC & NBIC
  • Coordinators:  Gabino Sanchez-Perez (WUR), Johan den Dunnen (LUMC), Hendrik-Jan Megens (WUR), Patrick Koks (WUR & NBIC)

This is the course website with all general information about this course. It will be updated when more information becomes available. You can find more information about previous editions, course materials, travel directions, etc. at the bottom of this page.
Application for this course is possible through the application form where specific information about this years issue of the course is available.
For more information about the application or logistics you can contact Patrick Koks.

A date for the 2014 edition has not been set yet.
Please refer to the pre-registration form to leave your name with us if you are interested in following this course or if you want to receive more information once available.


The de novo Assembly from NGS data course is organised by NBIC, LUMC and WUR for the first time in January 2013.  The course is targeted at PhD-students and PostDocs in Life Sciences or Bioinformatics with experience in Next Generation Sequencing techniques and data analysis. We will cover topics like sampling and statistics, the use of short– or long-read sequences, mate-pairs and having a (remotely related) reference genome or not; Quality assurance; the choice of assembler, data coverage. Gap closing, functional annotation and several other advanced aspects of de novo assembly will conclude this course. About half of the course is spent in practical workshops where you will learn how to perform a (small) assembly yourself. The aim of this course is for you to learn how to turn sequence data into meaningfull biology.

Target audience

This hands-on course is targeted at PhD's and researchers with experience in genomics or NGS data analysis. Participants will be expected to have experience in NGS data analysis or to have followed the NGS data analysis course.

Course Description

The advanced NGS de novo assembly course will build upon the Next-generation Sequencing course. De novo assembly from (short read) NGS data is challenging and may require tailored approaches for different complex genomes like those of polyploid plants.

About half of the course is devoted to theory and algorithms for de novo assembly on high throughput sequencing data and half to practical workshops where you will learn about the software implementations of these and carry out several steps of genome assembly using real data.

After a quick introduction into NGS techniques and platforms, this course will cover topics like: Sequencing strategies using short– or long-read sequences, paired-end and mate-pairs and having a (remotely related) reference genome or not. Elementary steps like Quality assurance and read filtering are essential and much of your results depend on the wise choice of the right algorithm and assembler with your specific type of data, data coverage and genome. Closing the gaps and finishing strategies, de novo transcriptomics, functional annotation and comparative genomics will conclude this course.

  • What type of reads (platform) do I need?
  • What sequencing depth do I need? Use of mate-pair libraries?
  • De novo assembly or use of a (remotely related) reference genome?
  • Work with an assembly pipeline or with separate command-line tools?
  • Limitation of current platforms and opportunuities of the near future?
  • How do I determine the quality of an assembly?
  • Strategies for full-sized genome assembly and complex cases?


Registration for this course has not been opened yet. a pre-registration form is available at:

By leaving your name and e-mail address and the course you'd like to attend, you help us with planning, organising and developing the optimal courses and course portfolio for bioinformatics and life sciences.


Creative Commons License

Lecture notes (slides) of the 2013 de novo Assembly Course in Wageningen

NBIC Advanced NGS Courses by Netherlands Bioinformatics Centre are licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. Based on a work at NBIC.

Tuesday January 8th, 2013

Wednesday January 9th, 2013