Time- and memory-efficient genome assembly with Raven

By Robert Vaser, Mile Sikic. Nature Computational Science, 2021

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Whole genome sequencing technologies are unable to invariably read DNA molecules intact, a shortcoming that assemblers try to resolve by stitching the obtained fragments back together. Here, we present methods for the improvement of de novo genome assembly from erroneous long reads incorporated into a tool called Raven. Raven maintains similar performance for various genomes and has accuracy on par with other assemblers that support third-generation sequencing data. It is one of the fastest options while having the lowest memory consumption on the majority of benchmarked datasets. Raven is designed to democratize genome assembly, being a simple and efficient tool while keeping high accuracy. Using a method for detection of false overlaps based on graph drawing, it can be employed for various genome sizes.

Subfields: Artificial Intelligence, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/e8956d923efe418fc65631073afea1ff662999d1