Resumen de Genome assembly of multiple genomes using long-read sequencing technologies
Adriano Muñoz Barrera
The emergence of long-read sequencing technologies has a substantial impact in genomic studies, facilitating de novo genome assembly, and structural variant detection in complex genomes. Accurate and complete de novo assembled genomes sustain variant identification and catalyze the discovery of new genomic features and functions and the effects in disease. However, accurate and precise de novo assemblies of large and complex genomes remains a challenging task. Long-read sequencing data alone or in hybrid mode combined with more accurate short-read sequences facilitate the de novo assembly of genomes. The main objective of this work is to unravel the potential of long-read sequencing technologies, specifically for de novo assembly, by the development of specific bioinformatics pipelines to reconstruct diverse types of genomes, from those of small viruses to the larger and more complex from humans. This comprehensive study aimed to achieve the following objectives: 1) To provide an updated review of current literature, technologies, and computational tools for Next-Generation and Third-Generation Sequencing to serve as the starting point at which the thesis develops; 2) To design, implement, and test bioinformatics strategies and pipelines for de novo assembly of viral genomes using short and long reads, assisting in the precise characterization of the Mpox outbreak of 2022; 3) To assess its potential for human mtDNA reconstruction and classification; and 4) To benchmark multiple state-of-the-art bioinformatics tools for de novo genome assembly of human whole genomes obtained with long reads, alone or in combination with short-read data, and develop and optimize a de novo assembly pipeline for human whole genomes. Overall, the results from this work highlight the transformative potential of long-read sequencing in de novo genome assembly, assisting in a rapid characterization of viral genomes involved in infectious diseases, and in unraveling complexities in human genomics in general, contributing from the basis to the development of biomedical research and to innovative diagnostic and therapeutic approaches.
