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TreeSeq, a Fast and Intuitive Tool for Analysis of Whole Genome and Metagenomic Sequence Data.

Authors :
Wintermans B
Brandt B
Vandenbroucke-Grauls C
Budding A
Source :
PloS one [PLoS One] 2015 May 01; Vol. 10 (5), pp. e0123851. Date of Electronic Publication: 2015 May 01 (Print Publication: 2015).
Publication Year :
2015

Abstract

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.

Details

Language :
English
ISSN :
1932-6203
Volume :
10
Issue :
5
Database :
MEDLINE
Journal :
PloS one
Publication Type :
Academic Journal
Accession number :
25933115
Full Text :
https://doi.org/10.1371/journal.pone.0123851