University of Saskatchewan Pulse Bioinformatics Core

Our Software

Our group has a strong focus on creating flexible, re-usable open-source software during the course of our work. While the main goals of this group include bioinformatic analysis and distribution of the data produced by the University of Saskatchewan Pulse Research group, an emphasis is placed on carrying out these goals through development of generic, re-usable, open-source tools in order to reduce the amount of repetition that can sometimes be a large part of a bioinfomaticists life. This has the added benefit of making our group more efficient and allowing us to give back to the larger bioinformatics community.

GBS PipelinePerl

The Genotype-by-Sequencing (GBS) Pipeline utilizes commonly-used open-source Bioinformatic tools for making SNP calls from raw GBS data. It aims to simplify the process while still providing a high level of flexibility to the user. Four commands are run to process raw Illumina paired-end reads through demultiplexing, trimming and filtering, alignment to a reference genome and SNP calling. Through the automatic generation of summaries at the end of each step, the user has the opportunity to evaluate their data and tweak parameters accordingly.

Our People

Lacey-Anne SandersonSenior Bioinformaticist & Web Developer

Lacey Sanderson is the innovator and main developer of KnowPulse, a breeder-focused web portal that integrates genetics and genomics of pulse crops with model legumes. KnowPulse was created as a means of distributing data generated by our group as well as amalgamating a variety of existing data to create a consistent platform for breeder-focused analysis. From the software side of things, KnowPulse is built using Drupal, an open source content management system, and Tripal, a Drupal module that handles display and management of biological data. Lacey has become a core developer of Tripal through her work on KnowPulse and has additionally wrote many Tripal Extension modules implementing breeder-specific functionality through the Tripal framework. Lacey received a Bachelor of Science (Major: Bioinformatics) and a Bachelor of Science (Major: Biology) from the University of Saskatchewan in 2009 before joining this group.

Larissa Ramsay Senior Bioinformaticist

Larissa worked for the National Research Council of Canada (NRC) Bioinformatics Centre before joining this group in 2013.

Carolyn Caron Junior Bioinformaticist

Carolyn has recently joined the group after completing her Bachelor of Science (Major in Bioinformatics) at the University of Saskatchewan. She helps analyze data for multiple projects as she works toward finding her niche. She has also developed an automated pipeline for analyzing Genotype-by-Sequencing (GBS) data.