Biewer Terrier dog breed WGS analysis pipeline development¶
🎯 Project objective¶
Internship project at the end of the DESS in bioinformatics.
Develop and document a DNA-seq gene variants identification pipeline
📋 Project description¶
In collaboration with a Veterinarian research laboratory for the CERMO-FC, aimed to identify genetic variants causing birth malformations causing prematured death in Biewer Terrier dog breed.
The data available were DNA-seq sequencing of prematurely dead individuals and their parents to compare gene expression and identify variants.
🎨 Implementation decisions¶
Study variant calling pîpelines
Develop Bash scripts for running variant calling pipeline steps on HPC cluster.
Computing resources from the Canadian Numerical Research Alliance were used.
Explore automation tools for tying together the pipeline steps
🧾 Key takeaway¶
Variant calling DNA-seq experience
Bash scripting skills development
HPC clusters experience with tasks parallelization and optimisation of resources