Genome assembly and bioinformatics with haplotypes

Bernardo Clavijo (Earlham Institute)
Thursday, February 15, 2018 - 10:30
Room Aurigny
Talk abstract: 

Producing and analysing de novo assemblies of complex organisms is now common across all life sciences. Still, these assemblies are mostly collapsed mosaics representing all haplotypes in single assembled regions. An excessive focus on contiguity has left precision and haplotype phasing as secondary concerns, despite advances in sequencing technologies that generate unprecedented amounts of information about haplotype composition.Here we will explore the possibilities and limitations of haplotype reconstruction on genome assembly, and the current trade-offs on assembly methods in different scenarios such as heterozygous and polyploid samples with short, long and linked reads. We will describe problems and solutions for the reconstruction and analysis of haplotypes in genome graphs. Finally, we will highlight the convergence of genetic and genomic evidence for haplotype studies and conclude with our vision of how the field could evolve in the near future.