TY - JOUR
T1 - TreeSeq, a fast and intuitive tool for analysis of whole genome and metagenomic sequence data
AU - Wintermans, B.B.
AU - Brandt, B.W.
AU - Vandenbroucke-Grauls, C.M.J.E.
AU - Budding, A.E.
N1 - With supporting information. - Corrections published in PLOS ONE 10(6): e0131379 and in PLOS ONE 10(7): e0133816.
PY - 2015/5/1
Y1 - 2015/5/1
N2 - 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.
AB - 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.
UR - https://doi.org/10.1371/journal.pone.0131379
UR - https://doi.org/10.1371/journal.pone.0133816
U2 - https://doi.org/10.1371/journal.pone.0123851
DO - https://doi.org/10.1371/journal.pone.0123851
M3 - Article
C2 - 25933115
SN - 1932-6203
VL - 10
JO - PLOS ONE
JF - PLOS ONE
IS - 5
M1 - e0133816
ER -