Nathaniel Brown

Nov 2, 2024 | biorxiv.org | Nathaniel Brown |Vikram S. Shivakumar |Ben Langmead |Johns Hopkins

AbstractCompressed full-text indexes enable efficient sequence classification against a pangenome or tree-of-life index. Past work on compressed-index classification used matching statistics or pseudo-matching lengths to capture the fine-grained co-linearity of exact matches. But these fail to capture coarse-grained information about whether seeds appear co-linearly in the reference. We present a novel approach that additionally obtains coarse-grained co-linearity ("chain") statistics.

May 22, 2024 | biorxiv.org | Stephen Hwang |Nathaniel Brown |Omar Ahmed |Katharine Jenike

AbstractPangenomes are growing in number and size, thanks to the prevalence of high-quality long-read assemblies. However, current methods for studying sequence composition and conservation within pangenomes have limitations. Methods based on graph pangenomes require a computationally expensive multiple-alignment step, which can leave out some variation. Indexes based on k-mers and de Bruijn graphs are limited to answering questions at a specific substring length k.