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This project built on past expertise to remedy a strategic gap in the availability of actively supported, scalable bioinformatics tools for genome assembly. The first objective was to develop a new alignment tool specialized in processing transcript and protein sequences, and optimized for the current generation of sequencing technology. The second objective was to build assembly assessment and annotation pipelines. This was a cutting-edge software engineering proposal, addressing strategic gaps in supporting bioinformatics tools for genome annotation. Its results could have a significant impact on genomics research done in BC and beyond and help secure BC’s place as an important bioinformatics hub.