Cracking the genomes of marine & non-model organisms: novel approaches for correcting, assembling and scaffolding genomic data using de Bruijn graphs and Hi-C contact maps

Venue: LGF, PGC building, A. Ma. Regidor St., University of the Philippines, Diliman, Quezon City, 1101

Date: Monday, 08 April 2019, 10:00 am (Manila Time)

Abstract

For a very long time, most bioinformatic tools for handling genome data have been geared toward haploid (or diploid but nearly homozygous) organisms such as humans, bacteria and laboratory strains of model species. As a result, these tools often perform very badly on highly heterozygous diploid or polyploid organisms, which is the case of many non-model and/or marine species. This presentation (followed by a short demonstration) will highlight tools that I have been developing in collaboration with computer scientists to deal with complex, heterozygous genomes in a computationally efficient manner:
Bcool (https://github.com/Malfoy/Bcool),
Bwise (https://github.com/Malfoy/Bwise)
and GRAAL (https://github.com/koszullab/instaGRAAL).

The first two tools use de Bruijn graphs to respectively correct genome data and assemble them, whereas the third one uses chromosome conformation capture (3C/Hi-C) contact maps to scaffold genome assemblies.

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