The aim of this course is to familiarise the participants with long read (also called “third generation”) sequencing technologies, their applications and the bioinformatics tools used to assemble this kind of data. Multiple sequencing platforms, including Pacific Biosciences and Oxford Nanopore MinION, are now available to generate reads that are several kilobases-long. It is also possible to assemble Illumina reads to generate in-silico long reads. These improvements have greatly facilitated the assembly of genomes but some other applications are emerging, for example, for haplotype phasing, or for the study of alternative splicing using RNA-seq.
This course will be composed of an introduction to the techniques and data analysis methods, a minisymposium and a hands-on session. The minisymposium will consist of short presentations by SIB researchers on the applications of these technologies. It will be followed by a panel discussion between speakers and the audience, letting the opportunity to debate on the advantages and pitfalls of these technologies for research projects. The hands-on session will consist of computer exercises that will enable the participants to familiarize with real datasets from different technologies and the bioinformatics tools to assemble genomes.