De Novo Assembly Tools: Research with Unbiased Engines - Renewal (DNA-TRUER)

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Summary This grant renewal proposal is about developing innovative new software that allow health researchers to take advantage of new advances in DNA sequencing. Over the last decade, technology advances have made DNA sequencing a routine and cost- effective method in many fields of life sciences research. The dominant technology at the start of our project generated millions of short sequences, consisting of 75-300 base pairs (the “letters” that make up the DNA sequence). These short “reads” have to be assembled in the right order to make sense of the data. Dr. Birol and his team are world leaders in genome assembly, and the award-winning software they have developed (with support from their existing NIH grant and other funding) has been used in diverse DNA sequencing projects, including The Cancer Genome Atlas project. Newer technologies are now available that generate information on much longer stretches of the input DNA as long or linked reads. Long read platforms can sequence over 100,000 base pairs per read, though with a relatively high error rate. Linked read platforms can associate multiple reads over similar lengths, although the data contains many gaps. Still, when coupled with bioinformatics tools that can leverage the rich information they provide, these new sequencing platforms open new frontiers in health research. Dr. Birol is seeking to extend his NIH funding support so that he and his team can be maintained to continue developing specialized software that quickly, accurately, and efficiently assemble and analyse long and linked sequence reads. These tools provide advanced capabilities in a range of projects, such as tracking infectious disease outbreaks, using genetic information to select the best drugs to treat an individual patient's cancer, and other applications. The new tools are being made available online free for other non-profit researchers to use in their own sequencing projects, allowing teams around the world to make faster progress in health research.