Eukatyotic Genome Assembly Using PACBIO (HIFI And CLR) And HI-C (Virtual Course)
Eukaryotic genomes may be composed of many repeats. Long reads sequencing technologies can span most of those repeats and produce genome assemblies with unprecedented contiguity. Further, sequencing technologies such as PacBio HiFi give us assembly contiguity and base accuracy. C hromatin conformation capture reads (Hi-C) bring the final information to scaffold assemblies into chromosomes.
This course will introduce the audience to a spectre of methods which are present in a usual assembly workflow, starting from raw data and finishing with a fully assembled genome. We will see how to manipulate raw reads, analyse their quality, how to run different assembly algorithms, how to run Hi-C scaffolding algorithms and how to analyse assembly quality.
Structured over five days, this course consists of both theoretical and practical aspects which are intertwined through each day. The presented theoretical foundation will be applied on small eukaryotic datasets. Due to the COVID-19 outbreak, this course will be held online.
TEACHING ASSISTANT: João Ferreira Nunes, MSc (Federal University of Rio de Janeiro, Brazil)