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- W4301358952 abstract "Genome assembly tools based on the de Bruijn graph framework rely on a parameter k, which represents a trade-off between several competing effects that are difficult to quantify. There is currently a lack of tools that would automatically estimate the best k to use and/or quickly generate histograms of k-mer abundances that would allow the user to make an informed decision. We develop a fast and accurate sampling method that constructs approximate abundance histograms with a several orders of magnitude performance improvement over traditional methods. We then present a fast heuristic that uses the generated abundance histograms for putative k values to estimate the best possible value of k. We test the effectiveness of our tool using diverse sequencing datasets and find that its choice of k leads to some of the best assemblies. Our tool KmerGenie is freely available at: http://kmergenie.bx.psu.edu/" @default.
- W4301358952 created "2022-10-05" @default.
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- W4301358952 date "2013-04-20" @default.
- W4301358952 modified "2023-10-18" @default.
- W4301358952 title "Informed and Automated k-Mer Size Selection for Genome Assembly" @default.
- W4301358952 doi "https://doi.org/10.48550/arxiv.1304.5665" @default.
- W4301358952 hasPublicationYear "2013" @default.
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