Son Hoang Nguyen

Efficient inference of large pangenomes with PanTA

PanTA efficiently constructs large bacterial pangenomes, outperforming existing tools in speed while maintaining accuracy and enabling progressive updates without rebuilding from scratch.

AMRomics: a scalable workflow to analyze large microbial genome collection

AMRomics is a scalable pipeline for analyzing large microbial genome collections, showing better performance than existing tools.

Pasa: Leverage population pangenome graph to scaffold prokaryote genome assemblies.

Pasa improves genome scaffolding by using population pangenome graphs, enhancing accuracy and efficiency for bacterial genome assemblies.

Real-time resolution of short-read assembly graph using ONT long reads

This paper introduces npGraph, a streaming hybrid assembly tool that improves genome assembly accuracy using ONT long reads and an assembly graph, while maintaining low computational cost.

Analysis of polyclonal vector integration sites using Nanopore sequencing as a scalable, cost-effective platform

The paper analyzes polyclonal vector integration sites using Nanopore sequencing to provide a scalable and cost-effective method for tracking gene-modified cells.

Evaluating the Genome and Resistome of Extensively Drug-Resistant Klebsiella pneumoniae using Native DNA and RNA Nanopore Sequencing

This study compares DNA and RNA nanopore sequencing for detecting drug resistance in XDR K. pneumoniae, finding RNA sequencing identifies more resistance genes and shows strong correlation with qRT-PCR.

Real-Time Demultiplexing Nanopore Barcoded Sequencing Data With npBarcode

npBarcode enables real-time demultiplexing of nanopore barcoded sequencing data with comparable accuracy to existing tools.

Scaffolding and Completing Genome Assemblies in Real-time with Nanopore Sequencing

This paper introduces a real-time method using nanopore sequencing to scaffold and complete genome assemblies, improving accuracy and reducing data and resource requirements.