Biozentrum 1, Hanns-Dieter-Hüsch-Weg 15, 55128 Mainz
Examination of the performance of nanopore sequencing applying different adaptive sampling approaches
Adaptive sampling is a selective sequencing technique for nanopore sequencing, enabling targeted real-time sequencing and enrichment of specific sequences without the need of prior sample preparation. It utilizes the ability of nanopore sequencers to reverse the current over a single nanopore and to reject the sample strand based on sequence composition.
For my master’s thesis, I analyze different microbial datasets, which were generated by using Oxford Nanopore Technologies’ (ONT) sequencing platforms (several publicly available datasets and a ZymoBIOMICS Microbial Community Standard sequenced by ourselves). As adaptive sampling is a promising method that can be exploited for enrichment of target species in such microbial samples, the optimization of known pipelines and workflows using this approach is of high interest. Therefore, the sequencing runs will be simulated in silico multiple times, improving run time parameters and downstream tools. Notably, an increase in quality and accuracy of targeted real-time sequencing has a variety of potential diagnostic applications.