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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 lar...

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Autores principales: Wintermans, Bastiaan B., Brandt, Bernd W., Vandenbroucke-Grauls, Christina M. J. E., Budding, Andries E.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4416914/
https://www.ncbi.nlm.nih.gov/pubmed/25933115
http://dx.doi.org/10.1371/journal.pone.0123851
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author Wintermans, Bastiaan B.
Brandt, Bernd W.
Vandenbroucke-Grauls, Christina M. J. E.
Budding, Andries E.
author_facet Wintermans, Bastiaan B.
Brandt, Bernd W.
Vandenbroucke-Grauls, Christina M. J. E.
Budding, Andries E.
author_sort Wintermans, Bastiaan B.
collection PubMed
description 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.
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spelling pubmed-44169142015-05-07 TreeSeq, a Fast and Intuitive Tool for Analysis of Whole Genome and Metagenomic Sequence Data Wintermans, Bastiaan B. Brandt, Bernd W. Vandenbroucke-Grauls, Christina M. J. E. Budding, Andries E. PLoS One Research Article 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. Public Library of Science 2015-05-01 /pmc/articles/PMC4416914/ /pubmed/25933115 http://dx.doi.org/10.1371/journal.pone.0123851 Text en © 2015 Wintermans et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Wintermans, Bastiaan B.
Brandt, Bernd W.
Vandenbroucke-Grauls, Christina M. J. E.
Budding, Andries E.
TreeSeq, a Fast and Intuitive Tool for Analysis of Whole Genome and Metagenomic Sequence Data
title TreeSeq, a Fast and Intuitive Tool for Analysis of Whole Genome and Metagenomic Sequence Data
title_full TreeSeq, a Fast and Intuitive Tool for Analysis of Whole Genome and Metagenomic Sequence Data
title_fullStr TreeSeq, a Fast and Intuitive Tool for Analysis of Whole Genome and Metagenomic Sequence Data
title_full_unstemmed TreeSeq, a Fast and Intuitive Tool for Analysis of Whole Genome and Metagenomic Sequence Data
title_short TreeSeq, a Fast and Intuitive Tool for Analysis of Whole Genome and Metagenomic Sequence Data
title_sort treeseq, a fast and intuitive tool for analysis of whole genome and metagenomic sequence data
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4416914/
https://www.ncbi.nlm.nih.gov/pubmed/25933115
http://dx.doi.org/10.1371/journal.pone.0123851
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