I live in Vancouver, Canada, where I'm a PhD candidate studying bioinformatics at the University of British Columbia with my supervisor, Inanc Birol. I work with the genome sequencing data of a variety of species, including human and the white spruce tree. I develop software that takes fragmented genome sequencing data and attempts to reassemble the original genome from which the short fragments were derived. My undergraduate degree is in computer engineering. I'm a programmer, an avid traveller, a singer, and an experimental amateur chef.

Automating data-analysis pipelines using R and Make

Slides and a hands-on activity

Slides and a hands-on activity ‘Automating’ comes from the roots ‘auto-‘ meaning ‘self-‘, and ‘mating’, meaning ‘screwing’. Bioinformatics analysis often involves designing a pipeline of commands and running that pipeline on many data sets. There are many ways to tackle this common task. Running commands interactively at the command line... [Read More]

UniqTag

Abreviate gene sequences to unique and stable identifiers

UniqTag is used to abbreviate gene sequences to unique and stable identifiers. It selects a representative k-mer from the sequence of each gene to be used as a systematic identifier for that gene. Unlike serial numbers, these identifiers are stable between different assemblies and annotations of the same data without... [Read More]

ABySS

Genome sequence assembler for large genomes

ABySS is a genome sequence assembler that distributes the computation of large genome sequence assembly over a cluster of computers using MPI. ABySS was used assemble the twenty gigabase white spruce (Picea glauca) genome, seven times the size of the human genome. [Read More]