Katharine Jenike

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.

Mar 11, 2024 | biorxiv.org | Sam Kovaka |Paul W. Hook |Katharine Jenike |Vikram S. Shivakumar

AbstractNanopore signal analysis enables detection of nucleotide modifications from native DNA and RNA sequencing, providing both accurate genetic/transcriptomic and epigenetic information without additional library preparation. Presently, only a limited set of modifications can be directly basecalled (e.g. 5-methylcytosine), while most others require exploratory methods that often begin with alignment of nanopore signal to a nucleotide reference.