Samuel Nicholls from the University of Birmingham in the UK presented at London Calling on “Long-read nanopore metagenomics for reconstruction of bacterial genomes.” They spoke about the impact of microbial communities on human health and the difficulties we encounter trying to culture some microbes. Nicholls and team published a study sequencing the Zymo mock communities. They used the long-read extraction techniques that others have developed. Nicholls is particularly interested in fecal transplant bacteriotherapy. The team did pilot studies with donor samples. They used Flye for assemblies and tried polishing. Nicholls was a bioinformatician who wrote Reticulatus to assemble metagenomes. The team used GPUs for acceleration. The pipeline was tested and compared to other workflows. Long-read metagenomics assemblies can be used to learn about the dynamics of the host. I will look into this program as it polishes sequences and provides a user-friendly workflow!
