Abstract

Advances in sequencing technologies over the last few decades have revolutionized the field of genomics, allowing for a reduction in both the time and resources required to perform de novo genome assembly. Until recently, second-generation sequencing technologies (also known as next generation sequencing (NGS)) produced highly accurate but short (up to 800bp) reads. These read lengths were not long enough to cope with the difficulties associated with repetitive regions. Today, so-called third-generation sequencing (TGS) technologies, also known as single-molecule real-time (SMRT) sequencing, have become dominant in de novo assembly of large genomes. TGS can use native DNA without amplification, reducing sequencing error and bias,. In 2020, PacBio introduced high fidelity (HiFi) sequencing, which produces reads 10-25 kbp in length with a minimum accuracy of 99% (Q20). In this tutorial, you will use HiFi reads in combination with data from additional sequencing technologies to generate a high-quality genome assembly.

About This Material

This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.

Questions this will address

• What combination of tools can produce the highest quality assembly of vertebrate genomes?
• How can we evaluate the quality of the assembly in a reference-free way?

Learning Objectives

• Learn the tools necessary to perform a de novo assembly of a vertebrate genome
• Evaluate the quality of the assembly