StrainGE: a toolkit to track and characterize low-abundance strains in complex microbial communities

Human-associated microbial communities comprise not only complex mixtures of bacterial species, but also mixtures of conspecific strains, the implications of which are mostly unknown since strain level dynamics are underexplored due to the difficulties of studying them. We introduce the Strain Genome Explorer (StrainGE) toolkit, which...

Mycobacterium tuberculosis genomics: The Next Generation

This thesis represents one small step in the battle with TB, where we apply WGS approaches to explore different topics of TB research. Here we offer the global community a method to diagnose complex TB infections consisting of multiple distinct strains. We show that this functionality is necessary and has been overlooked by the TB community in...

An educational guide for nanopore sequencing in the classroom

The last decade has witnessed a remarkable increase in our ability to measure genetic information. Advancements of sequencing technologies are challenging the existing methods of data storage and analysis. While methods to cope with the data deluge are progressing, many biologists have lagged behind due to the fast pace of computational...

QuantTB- A method to classify mixed Mycobacterium tuberculosis infections within whole genome sequencing data

Background: Mixed infections of Mycobacterium tuberculosis and antibiotic heteroresistance continue to complicate tuberculosis (TB) diagnosis and treatment. Detection of mixed infections has been limited to molecular genotyping techniques, which lack the sensitivity and resolution to accurately estimate the multiplicity of TB infections. In...

Computational Methods for Strain-Level Microbial Detection in Colony and Metagenome Sequencing Data

Metagenomic sequencing is a powerful tool for examining the diversity and complexity of microbial communities. Most widely used tools for taxonomic profiling of metagenomic sequence data allow for a species-level overview of the composition. However, individual strains within a species can differ greatly in key genotypic and phenotypic...