VarDetect statistics

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Citations per year

Number of citations per year for the bioinformatics software tool VarDetect
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Tool usage distribution map

This map represents all the scientific publications referring to VarDetect per scientific context
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VarDetect specifications

Information


Unique identifier OMICS_15081
Name VarDetect
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Input data A reference sequence
Input format FASTA, XML
Output data List of predicted SNPs
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Stability Stable
Requirements
JRE
Maintained Yes

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Maintainer


  • person_outline Sissades Tongsima

Publication for VarDetect

VarDetect citations

 (4)
library_books

Whole Genome Sequencing Reveals Complex Evolution Patterns of Multidrug Resistant Mycobacterium tuberculosis Beijing Strains in Patients

2013
PLoS One
PMCID: 3855793
PMID: 24324807
DOI: 10.1371/journal.pone.0082551

[…] All polymorphisms differentiating serial isolates and genes associated with acquired drug resistances were further validated by Sanger sequencing using an ABI3130xl Sequencer. In addition, we applied VarDetect (vers. 200601251500) [] to analyze peak height ratios of heterogeneous SNPs in order to estimate the frequency of different dominating subpopulations in all serial patient derived isolates ( […]

library_books

A Simple Strain Typing Assay for Trypanosoma cruzi: Discrimination of Major Evolutionary Lineages from a Single Amplification Product

2012
PLoS Negl Trop Dis
PMCID: 3409129
PMID: 22860154
DOI: 10.1371/journal.pntd.0001777

[…] cVI.As proposed, the assay requires an accurate call of heterozygous peaks for hybrid strains, something that is easily done with free software packages, such as PolyPhred (free for academic use) or VarDetect . However, if necessary to avoid the calling of heterozygous (double) peaks, this procedure can be substituted by a more laborious strategy of cloning and sequencing a number of amplificatio […]

library_books

Atypical epigenetic mark in an atypical location: cytosine methylation at asymmetric (CNN) sites within the body of a non repetitive tomato gene

2011
BMC Plant Biol
PMCID: 3117769
PMID: 21599976
DOI: 10.1186/1471-2229-11-94

[…] cts were purified using gel electrophoresis and a QIAquick Gel Extraction Kit (Qiagen) and sequenced without previous subcloning using the same primers used for PCR. Chromatograms were analysed using VarDetect [] to estimate the ratio of cytosine to thymine signal. Statistical analysis was performed using the Mann-Whitney test at the 95% significance level. […]

library_books

Emerging strengths in Asia Pacific bioinformatics

2008
BMC Bioinformatics
PMCID: 2638166
PMID: 19091008
DOI: 10.1186/1471-2105-9-S12-S1

[…] Single nucleotide polymorphisms (SNPs) are key elements in genomics research, importantly for correlating genetic variations with disease outcomes. VarDetect (Ngamphiw et al. []) is a new generation tool for the accurate detection of SNPs, while the functional implications of these variations can be assessed using FANS (Liu et al. []). […]


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VarDetect institution(s)
Genome Institute, National Center for Genetic Engineering and Biotechnology, Pathumthani, Thailand; Department of Computer Science, School of Engineering and Technology, Asian Institute of Technology, Pathumthani, Thailand; Division of Medical Genetics, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
VarDetect funding source(s)
This project was supported by Genalys program done by the Centre National de Genotypage (CNG) and the National Center for Genetic Engineering and Biotechnology (BIOTEC). It was also funded by the Thailand Research Fund (TRF) through the Royal Golden Jubilee Ph.D. Program (Grant No. PHD/4.I.MU.45/C.1) and by the Junior Science Talent Program scholarship awarded by the National Science and Technology Development Agency (NSTDA), Thailand.

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