TreeSeq, a Fast and Intuitive Tool for Analysis of Whole Genome and Metagenomic Sequence Data.
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.
Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands.
Bastiaan
B
Wintermans
Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and VU University Amsterdam, Amsterdam, The Netherlands.
Bernd
B
Brandt
Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands.
Christina
C
Vandenbroucke-Grauls
Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands.
Andries
A
Budding
D005243:Feces / Q000382:microbiology; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D007709:Klebsiella / Q000235:genetics; D056186:Metagenomics / Q000379:methods*; D064307:Microbiota / Q000235:genetics; D010641:Phenotype; D012984:Software