Assembling the zebrafish genome with long-read sequencing

Although long-read sequencing has been used to resolve multiple vertebrate genomes, assembling a de novo genome is still challenging for most researchers. In this webinar, Yelena Chernyavskaya outlined her team's protocol for obtaining high molecular weight samples required for long-read assemblies and compared two commonly used assembler packages to reconstruct the zebrafish genome.

Their long-read assembly improved the resolution of the reference genome and identified novel sites of retrotransposon integration previously unreported in the current reference assembly.

The pipeline presented can easily be modified and applied to assemble any vertebrate genome regardless of prior bioinformatics expertise.

Watch to learn:

• The drawbacks of original assemblies made with shotgun and short-read sequencing
• How long-read sequencing can overcome assembly issues
• See a side-by-side comparison of several pipelines that can be used to assemble a new genome
• See examples of how to uncover novel differences presented by new assemblies

Meet the speaker

Yelena Chernyavskaya, Research Scientist, University of Kentucky Department of Molecular and Cellular Biochemistry

Yelena’s research has always centered around zebrafish. She received her PhD from Colorado State University (CO, USA) and went on to do a postdoc in New York at Mount Sinai Hospital (NY, USA) and NYU Abu Dhabi (UAE), where she studied how pathologies such as cancer and autoimmune disease could be driven by dysregulation of different epigenetic factors which activated latent retro-transposons within the cell. Currently, her work with (Dr.) Jessica Blackburn involves developing new zebrafish models and technologies for studying childhood cancers such as Acute Lymphoblastic Leukemia (ALL) and Diffuse Intrinsic Pontine Glioma (DIPG).