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Protocols

snpTree specifications

Information


Unique identifier OMICS_21963
Name snpTree
Software type Pipeline/Workflow
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 1.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline Pimlapas Leekitcharoenphon

Publication for snpTree

snpTree citations

 (15)
library_books

Phenotypic and Genotypic Eligible Methods for Salmonella Typhimurium Source Tracking

2017
Front Microbiol
PMCID: 5744012
PMID: 29312260
DOI: 10.3389/fmicb.2017.02587

[…] tree from assembled genomes or sets of sequence reads just by a mere upload of data. among the tools which accept raw sequence reads and performs basics bioinformatics analysis also include snptree (leekitcharoenphon et al., ), nucleotide difference tree (ndtree) (leekitcharoenphon et al., ) and csi phylogeny (kaas et al., ). interestingly, these techniques exclude a significant […]

library_books

In Vitro Tolerance of Drug Naive Staphylococcus aureus Strain FDA209P to Vancomycin

2017
Antimicrob Agents Chemother
PMCID: 5278750
PMID: 27855063
DOI: 10.1128/AAC.01154-16

[…] to detect genetic alterations in the survivor strains, the 250-bp paired-end sequencing reads were mapped to the complete reference genome sequence of parental strain fda209p () using the programs snptree (v1.1) and csi phylogeny (v1.1) (). the average percentage of the reference genome mapped was 99.94%, indicating that the number of reads in this analysis was sufficient., the detected […]

library_books

Genome Sequence of Airborne Acinetobacter sp. Strain 5 2Ac02 in the Hospital Environment, Close to the Species of Acinetobacter towneri

2016
Genome Announc
PMCID: 5146438
PMID: 27932646
DOI: 10.1128/genomeA.01343-16

[…] (2014), and disinfectant susceptibility testing was performed by microdilution. phylogenetic analysis was carried out by average nucleotide identity (ani), single nucleotide polymorphism analysis (snptree), and rna polymerase beta subunit sequence (rpob) analysis. a matrix-assisted laser desorption ionization–time of flight mass spectrometry (maldi-tof ms) dendrogram was generated (bruker […]

library_books

Parallel Evolution in Streptococcus pneumoniae Biofilms

2016
Genome Biol Evol
PMCID: 4898793
PMID: 27190203
DOI: 10.1093/gbe/evw072

[…] position, and quality metrics. variants were filtered based on quality score (q value) and those with q values <20 were rejected. alternatively, variant call files (.vcf) were generated using snptree1.1 (). each mutation was manually curated by mapping the illumina fastq files against the wt reference to generate bam files (.bam) and indexed bam files (.bai) using samtools. bam files […]

library_books

Detection, Characterization, and Typing of Shiga Toxin Producing Escherichia coli

2016
Front Microbiol
PMCID: 4828450
PMID: 27148176
DOI: 10.3389/fmicb.2016.00478

[…] scotland and public health england., the serum staten institute in copenhagen, denmark sequenced 42 isolates received in a 7-week period and determined their relationship using their web-based tools snptree and ndtree (joensen et al., ). during this study period they had an outbreak with 13 cases of e. coli o157:h7, six of which were included in their study. the ndtree method, an assembly-free […]

library_books

Identification of a Latin American specific BabA adhesin variant through whole genome sequencing of Helicobacter pylori patient isolates from Nicaragua

2016
BMC Evol Biol
PMCID: 4770546
PMID: 26928576
DOI: 10.1186/s12862-016-0619-y

[…] used can be found in additional file : table s3., phylogenetic trees were created in two different ways to reflect different sequence relationships. the whole-genome snp tree was created using the snptree web interface []. snptree is based on snp calling with the mummer v3 software [] and fasttree [] for tree construction. the isolate southafrica7 was used as reference genome, since […]


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snpTree institution(s)
National Food Institute, Technical University of Denmark, Lyngby, Denmark; Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Denmark
snpTree funding source(s)
Supported by the Center for Genomic Epidemiology (09- 067103/DSF), Danish Food Industry Agency (3304-FVFP-08) and the Technical University of Denmark.

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