Vikram S Shivakumar

Minimizer 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...

Aligning genomes into common coordinates is central to pangenome analysis and construction, but it is also computationally expensive. Multi-sequence maximal unique matches (multi-MUMs) are guideposts for core genome alignments, helping...

Compressed 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...

Summary: Improvements in nanopore sequencing necessitate efficient classification methods, including pre-filtering and adaptive sampling algorithms that enrich for reads of interest. Signal-based approaches circumvent the computational bottleneck of basecalling. But...

Improvements in nanopore sequencing necessitate efficient classification methods, including pre-filtering and adaptive sampling algorithms that enrich for reads of interest. Signal-based approaches circumvent the computational bottleneck of basecalling. But past...

Plants in the Burseraceae are globally recognized for producing resins and essential oils with medicinal properties and have economic value. In addition, most of the aromatic and non-aromatic components of...

The curry tree (Bergera koenigii L.) is a widely cultivated plant used in South Asian cooking. Next-generation sequencing was used to generate the transcriptome of the curry leaf to detect...

The Clauseneae (Aurantioideae, Rutaceae) is a tribe in the Citrus family that, although economically important as it contains the culinary and medicinally-useful curry tree (Bergera koenigii), has been relatively understudied....