Genome assembly: from reads to high-quality chromosome-level genomes
In this 18-hour course, participants will be taken through the whole process involved in obtaining a high-quality reference genome for their species of interest. This is, from whole-genome sequencing data to a high-quality chromosome-level assembly.
Our course introduces the participants to the concept of genome assembly and explores the different approaches and possibilities for every step of the process. We will cover the approaches taken with data from all available technologies (Illumina, Pacbio -HiFi and CLR-, and Oxford Nanopore), as well as the use of proximity-ligation data (Hi-C) to obtain chromosome-level assemblies. We will cover important steps such as pre-assembly genome characterisation using k-mers, and assembly QC using different bioinformatic tools (Merqury, BUSCO, Pretext, etc). Finally, the concept of genome annotation, as well as annotation pipelines and approaches will be introduced.
By the end of the course, participants will be able to comprehend the decision making involved in the assembly process, to understand the different approaches, interpret their outputs and evaluate the quality of genome assemblies. They will also get a general idea of how the genome annotation process works.
The course will combine theory with hands-on exercises using real datasets. We will offer consultation on the participant’s own data and results during the course.
- Language: English.
- Number of places available: 18.
- Instructors: Dr Lucía Campos-Domínguez, Jaime Imaz, and Antón Vizcaíno.
Target audience and requirements
Master's students, early career researchers (pre-docs and post-docs), or senior researchers, either from Industry or Academia, interested in genome sequencing. Please note that this is an introductory course and is not intended for researchers with experience in genome assembly and annotation.
Basic skills in high-throughput sequencing are required. Researchers who are not familiar with high-throughput sequencing might want to consider signing up first to our introductory course.
Basic use of UNIX-based command line is desirable. Hands-on work will be performed in UNIX environments (Linux, Mac).
All participants should bring and use their own laptops. Software packages and datasets used during the course will be provided to the participants via a virtual machine, that will be installed before the beginning of the course.
An attendance certificate will be provided at the end of the course.