Introduction

Next-generation sequencing is not yet commonly used in clinical laboratories because of a lack of simple and intuitive tools. We developed a software tool (TreeSeq) with a quaternary tree search structure for the analysis of sequence data. This permits rapid searches for sequences of interest in large datasets. We used TreeSeq to screen a gut microbiota metagenomic dataset and a whole genome sequencing (WGS) dataset of a strain of Klebsiella pneumoniae for antibiotic resistance genes and compared the results with BLAST and phenotypic resistance determination. TreeSeq was more than thirty times faster than BLAST and accurately detected resistance gene sequences in complex metagenomic data and resistance genes corresponding with the phenotypic resistance pattern of the Klebsiella strain. Resistance genes found by TreeSeq were visualized as a gene coverage heat map, aiding in the interpretation of results. TreeSeq brings analysis of metagenomic and WGS data within reach of clinical diagnostics.

Publications

  1. TreeSeq, a Fast and Intuitive Tool for Analysis of Whole Genome and Metagenomic Sequence Data.
    Cite this
    Wintermans B, Brandt B, Vandenbroucke-Grauls C, Budding A, 2015-01-01 - PLoS ONE

Credits

  1. Bastiaan Wintermans
    Developer

    Department of Medical Microbiology and Infection Control, VU University Medical Center

  2. Bernd Brandt
    Developer

    Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA)

  3. Christina Vandenbroucke-Grauls
    Developer

    Department of Medical Microbiology and Infection Control, VU University Medical Center

  4. Andries Budding
    Investigator

    Department of Medical Microbiology and Infection Control, VU University Medical Center

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Summary
AccessionBT000272
Tool TypeApplication
Category
Platforms
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByAndries Budding