Assembly And Annotation Of Genomes (Virtual Course)
This course will introduce biologists and bioinformaticians to the concepts of de novo assembly and annotation, providing a theoretical framework and practical examples. A variety of sequencing technologies and their applications to generate high-quality reference genomes will be presented and discussed. They include Illumina short reads (for both assembly and gene annotation), PacBio HiFi (‘High Fidelity’) and CLR (‘Continous Long Read’) reads, Oxford Nanopore long and ultralong reads, as well as scaffolding technologies including optical mapping and proximity ligation (Hi-C). Special attention will be given to quality control throughout the assembly process (e.g. tools such as Genomescope, Merqury, Pretext) as well as to consensus and structural error mitigation. Annotation tools using Illumina RNA-Seq and Pacbio IsoSeq data will be introduced. By the end of the course the students will be able to understand what is needed to generate an annotated reference genome of high-quality. Due to the COVID-19 outbreak, this course will be held online.