Sequence Assembly Lecture

Overview

Teaching: 60 min
Exercises: 0 min

Questions

• How can the information in the sequencing reads be reduced?

• What are the different methods for assembly?

• How can we assess the quality of an assembly?

Objectives

• Understand differences between assembly methods

• Understanding different assembly quality analysis methods

Sequence assembly and assembly quality

Once your assembly has started, you can follow the lecture by Professor Bas Dutilh. As it is difficult to time when everyone is ready for the lecture and genome assembly is very time consuming, we decided to make use of a prerecorded lecture. Slide handouts are available at https://klif.uu.nl/klif/mgen/MicrobialGenomics_AssemblyStrategies_Linda.pdf

This lecture details assembly strategies, different kind of assemblers and ways of assessing assembly quality and binning of contigs when doing metagenomic assembly. After the assembly lecture there is a lunch break. If you have any questions please put up your hand. You should be able to answer the question why a short k-mer (21 bp in our example) results in a poorer assembly than a longer k-mer (e.g. 55 bp). You should also know the difference between the contigs and the scaffolds.

The lecture can be found here: https://www.youtube.com/watch?v=mHmMbPxKmn0

The lecture takes 60 minutes.

Key Points

• Assembly is a process which aligns and merges fragments from a longer DNA sequence in order to reconstruct the original sequence.

• k-mers are short fragments of DNA of length k

• Quality can be assessed using N50 but also using other methods