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Publications of the Week

ntJoin: Fast and Lightweight Assembly-Guided Scaffolding Using Minimizer Graphs

By May 7, 2020No Comments

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This week we profile a recent publication in Bioinformatics from Dr. René Warren (pictured
above) and Dr. Inanc Birol (below) at Canada’s Michael Smith Genome Sciences Centre.

Can you provide a brief overview of your lab’s current research focus?

Inanc Birol

Dr. Inanc Birol

The Bioinformatics Technology Lab at Canada’s Michael Smith Genome Sciences Centre (GSC) at BC Cancer, led by GSC Distinguished Scientist Dr. Inanc Birol, is a computational biology research group. We develop novel algorithms, data structures and genome analysis software and offer a complete and scalable solution for de novo genome assembly. The bioinformatics tools we build find applications in cancer research, and are the foundation of our genome research program at the GSC.

What is the significance of the findings in this publication?

This publication introduces a new bioinformatics tool, ntJoin, which is now available for researchers to freely download and use. ntJoin is a rapid and lightweight tool for genome assembly scaffolding that leverages minimizer sketches, simultaneously making it faster while reducing the amount of memory needed in comparison to existing state-of-the-art tools.

What are the next steps for this research?

We are continually working on improving and developing new and exciting bioinformatics technologies with applications in genomics and transcriptomics. For ntJoin, we are exploring the development of additional features to improve its performance on highly repetitive genomes such as that of spruce, which has been the prime focus of a Genome Canada-funded large scale applied research project in collaboration with the Michael Smith Laboratories at UBC, Natural Resource Canada, Université Laval, the BC Ministry of Forests and the GSC.

This work was funded by:

This work was supported by Genome BC, Genome Canada, and the National Institutes of Health.

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