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Ryan Wick

Assembly is still hard: challenges in genome assembly in the era of long reads

About Ryan Wick

Ryan Wick received a BSc from the University of Wisconsin–Madison and a Master’s in Bioinformatics from the University of Melbourne. He currently works in the Holt Lab at the University of Melbourne’s Centre for Systems Genomics. Ryan is particularly interested in de novo assembly and is the creator of Bandage, an interactive assembly graph viewer, and Unicycler, a hybrid assembly tool for bacterial genomes.

Abstract

Genome assemblers are tools which aim to reconstruct an original genome from sequencing reads. A ‘perfect’ assembler would take only reads as input and output a complete, error-free genome. This goal is usually impossible with short read sequencing, but long reads from Oxford Nanopore sequencers bring it tantalisingly close. While long reads are enormously helpful for assembly, issues remain. In this talk, I will describe the various ways an assembly can fail: sequence inaccuracy, incomplete or misassembled sequences, and lost variation. For each, I will discuss the underlying causes and what future developments are necessary to overcome them and bring us closer to perfect assemblies.
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