[VanBUG] Thursday, Oct 13, 6pm – Inanc Birol, Haploid Assembly of Diploid Genomes‏

Please post poster available at http://vanbug.org
Next VanBUG (Vancouver Bioinformatics User Group) talk is on Thursday,
October 13 at 6pm. The seminar is followed by pizza, refreshments and
great networking.

*Intro speaker* (10mins): Olena Morozova, PhD Candidate, Marra Lab,
Genome Sciences Centre, BC Cancer Agency
A wide spectrum of somatic mutation in high-risk neuroblastoma

*Featured speaker*: Inanc Birol, Bioinformatics Group Leader, Genome
Sciences Centre, BC Cancer Agency and Adjunct Professor, School of
Computing Science, Simon Fraser University

Haploid Assembly of Diploid Genomes

Most assembly algorithms in use have an implicit assumption that a
sequenced nucleic acid has a haploid-like structure, or at worst that
the sequence representing a genomic location is present with a high
similarity in the read data. This assumption holds nicely in the case of
model organisms, which are usually inbred to reduce haplotypic
diversity, and is even not challenged significantly in the case of human
samples because of an evolutionarily recent population bottleneck our
species experienced. However, when an organism of interest has a diploid
genome with a pronounced distance between haplotypes, or when an
environmental sample is investigated that represents a collection of
similar species, the assumption fails.

Furthermore, read lengths of popular high throughput sequencing
technologies, and even the spatial associations brought by paired end
reads are often not enough to completely de-phase the assembled
sequences. In this talk, I will discuss the particular challenges one
faces during de novo assembly of such datasets, and describe how we
approach to their solution within the ABySS framework.

ABySS is a short read assembly tool, particularly developed to address
large scale assembly problems. I will introduce how it handles distance
information to extend and scaffold contigs, and how it represents
haplotypic information in its output. I will demonstrate its performance
on the assembly of the mountain pine beetle genome.

Please note:
Trainees are invited to meet with the VanBUG speaker for open discussion
of both science and career paths. This takes place 4:30-5:30pm in either
the Boardroom or Lunchroom on the ground floor of the BCCRC

Recommended Reading

675 West 10th Avenue
Gordon and Leslie Diamond Family Theatre
BC Cancer Agency

Start Date: 13/10/2011
Start Time: 6:00 PM
End Time: 7:30 PM

Contact Name:
Stefanie Butland

The VanBUG team:
Stefanie Butland
Cedric Chauve
Bhavjinder Dhillon
Elodie Portales-Casamar

VanBUG is generously sponsored by the CIHR Bioinformatics Training
Program, MITACS, GenomeBC, and the Canadian Bioinformatics Workshops

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