software

Squeegee is the first computational method for identifying potential microbial contaminants in the absence of environmental negative control samples.

Variabel is the first method designed for rescuing low frequency intra-host variants from ONT data alone.

Vulcan is the first long-read mapping framework that combines two distinct gap penalty modes for improved structural variant recall and precision.

Tracking SARS-CoV-2 variants within the Harvest Software Suite

Check out the SeqScreen preprint here

A novel approach to inferring microbial interactions across multiple microbiome samples

Dynamics of Colonization and Infection by Multidrug-resistant Pathogens in Immunocompromised and Critically Ill Patients

Background 16S rRNA based analysis is the established standard for elucidating microbial community composition. While short read 16S analyses are largely confined to genus-level resolution at best since only a portion of the gene is sequenced, full-length 16S sequences have the potential to provide species-level accuracy.

Taxonomy-Oblivious Graph-Based Characterization of Genome Dynamics in Microbial Communities.