Improving high-continuity plant de novo nanopore assemblies towards chromosome-scale reference genomes

Max Schmidt

Max Schmidt, Research Center Juelich


Oxford Nanopores sequencing technology has enabled us to generate high quality contig assemblies in the megabase contig N50 range. After polishing these genomes with the original nanopore reads using tools like Medaka and Racon, we are now employing different methods like Hi-C, pore-C and optical mapping to turn those assemblies into chromosome scale scaffolded assemblies. The combination of nanopore long-read assemblies and Hi-C even allowed us to generate haplotype phased chromosome assemblies. Using Oxford Nanopore Technologies new Chromosome conformation capture technique pore-C, we were also able to generate chromosome scale assemblies using nothing, but sequencing data generated on Oxford Nanopore-platforms even for larger genomes.


Maximilian Schmidt was awarded a BSc. in Biotechnology from the University of Cooperative Education Riesa in 2012 before moving to RWTH Aachen to complete a MSc, where he studied genes involved in plant cell wall biosynthesis. He is currently a PhD student with Professor Usadel at RWTH Aachen where he is interested in de novo plant genome sequencing. Recently he moved together with Björn Usadel and his group to the Research Center Jülich. Maximilian has worked with nanopore sequencing technology since 2016 and has been part of the group that published the first eukaryotic genome with Oxford Nanopore technology in 2017.