INB-Lunch-Seminar

Applying second generation sequencing to Malaria

Thomas D. Otto

After a quick introduction to second generation sequencing, I will
explain a set of tools for improving assemblies. In particular, we now
use deep coverage Illumina data to iteratively improve the accuracy of
underlying reference sequences, accurately define error-prone regions
and to walk into gaps. We also use comparative genomics to order and
orientate contigs and transfer annotation from genome to genome. In
the last part of my talk, I will discuss how to use these tools to
find differences between two isolates of a Malaria strain and detect,
for example, drug resistance or different phenotypes. Finally, I will
present RNA-Seq results in Malaria.