Vikram S. Shivakumar

Jan 8, 2025 | biorxiv.org | Alan Zheng |Ishmeal Lee |Vikram S. Shivakumar |Omar Ahmed

AbstractMinimizer digestion is an increasingly common component of bioinformatics tools, including tools for De Bruijn-Graph assembly and sequence classification. We describe a new open source tool and library to facilitate efficient digestion of genomic sequences. It can produce digests based on the related ideas of minimizers, modimizers or syncmers. Digest uses efficient data structures, scales well to many threads, and produces digests with expected spacings between digested elements.

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.

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.