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Showing 1 to 4 of 4 for “"genome graph"”.
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Genome-graph based genotyping with applications to highly variable genes in P. falciparum
Analysing genetic variation in pathogen genomes is key to understanding their biology, evolution and epidemiology. Typically, this is done by assembling one arbitrary genome, defined as the ‘reference’, and describing other samples as deviations from it. However, this model breaks down in highly …
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Examining bacterial variation with genome graphs and Nanopore sequencing
… found within a given species is called the pan-genome and is generally much larger than the gene repertoire of a single cell. A consequence of this pan-genome is that bacterial genomes are highly adaptable and thus variable. The dominant paradigm for analysing genetic variation relies on a …
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Function-based Algorithms for Biological Sequences
… to operate on. Due to continuous progress in genome sequencing, genome rearrangements and construction of evolutionary genome graphs, which represent the relationships between genomes, become challenging tasks. Previous approaches are largely based on distance measure so that relationship …
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Graphical pangenomics
Completely sequencing genomes is expensive, and to save costs we often analyze new genomic data in the context of a reference genome. This approach distorts our image of the inferred genome, an effect which we describe as reference bias. To mitigate reference bias, I repurpose graphical models …