Advanced de novo assembly and resolving complex genomic regions

This course covers topics on what every biologist should know about de novo assembly and study design, overview of available technologies and sampling strategies, methodologies and framework for de novo assembly (haploid and polyploid genomes), gap closure, quality assessment and functional annotation. In addition, we will showcase recent achievements, novel discoveries and current limitations in resolving complex genomes. The practical sessions are designed in such a way to promote lively discussions on how to design your study, the best practices, dos and don’ts, and provide you with an outlook on how to move from sequencing data to high-quality assembly and meaningful biological interpretation. After following this course, participants will gain insights on how to design a genome assembly study and will have an overview of challenges and various techniques to choose the most fitting strategy in order to produce a high-quality genome assembly.

Date: June 1-3,  2015

Target audience: This course is targeted at PhD students and Postdocs in Life Sciences or Bioinformatics with basic knowledge of next-generation sequencing (NGS) technology and data analysis.


Reconstructing a genome from a collection of significantly shorter sequencing reads constitutes a de novo genome assembly process. In spite of its importance to biology, high-quality genome assembly is a challenging process and often requires careful study design and complementary strategies to reliably resolve complex genomes, such as those of polyploid or repeat-rich eukaryotes. This course is aimed at providing a framework on sampling and study design, the choice of sequencing strategy and appropriate assembly approaches, insightful assessment and evaluation of the draft assembly, as well as potential complementary approaches for resolving complex regions and closing persistent gaps in the genome. In addition, we also cover topics on functional annotation of the genome, de novo transcriptomics and comparative genomics to further aid the biological interpretation.

This three-day course is structured according to four main themes:

  • What should every biologist know about de novo assembly
  • Technologies
  • Achievements, novel discoveries and current limitations
  • Available methodologies, strategies and common mistakes

Each day will be concluded by a keynote from a distinguished scientist in the field to leave the audience with an outlook on successful stories and future directions. Practical sessions are designed in such a way to encourage lively discussions on how to perform different steps of the genome assembly process as well as how to interpret the outcomes and spot often overlooked but common mistakes.

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