KvarQ protocols

View KvarQ computational protocol

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KvarQ specifications

Information


Unique identifier OMICS_05974
Name KvarQ
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C, Python
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for KvarQ

KvarQ in pipeline

2017
PMCID: 5604961
PMID: 28926571
DOI: 10.1371/journal.pone.0184510

[…] snvs in the core genome with raxml using a general time-reversible model of substitution []. the phylogenetic tree was visualized with figtree and manually annotated., the user-friendly web tools kvarq, phyrese and tbprofiler were used to infer phylogenetic lineage from sequencing reads [–]. kvarq classified samples into the seven global lineages, while phyrese and tbprofiler offered […]


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KvarQ in publications

 (5)
PMCID: 5365657
PMID: 28137812
DOI: 10.1128/AAC.02169-16

[…] after uptake in clinical settings (, , ). importantly, this also applies to software tools designed to automate the analysis of whole-genome sequencing data. in fact, three of the current tools (kvarq, mykrobe predictor tb, and tb profiler) misclassified strain btb-08-045 with gyra t80a+a90g as resistant to at least one fluoroquinolone because the respective mutation catalogues […]

PMCID: 5238942
PMID: 27798628
DOI: 10.1038/ng.3704

[…] coverage and genetic diversity among l4.6.1/uganda strains, we analyzed all available wgs data from several published studies,–, and other whole genome data available in the public domain. we used kvarq to screen for the l4.6.1/uganda-specific snps described below. starting from 13,067 genome sequences and excluding all clustered isolates except for one representative of each cluster, […]

PMCID: 4982626
PMID: 27518818
DOI: 10.1371/journal.pone.0160992

[…] those remaining and satisfying all the above criteria were regarded as high-confidence snps., genetic markers associated with drug-resistant tb were detected using tb-profiler [], phyresse [], kvarq [] and phytb []. novel resistance-associated marker candidates were determined by comparative genomics between serial isolates of mtb which had exhibited a change from susceptible to resistant […]

PMCID: 4446134
PMID: 26019726
DOI: 10.1186/s13073-015-0164-0

[…] six datasets was performed and analytical sensitivities and specificities of the inferred resistance relative to the reported phenotype were compared (figure , additional file : figures s3 and s4). kvarq [], a new tool that directly scans fastq files of bacterial genome sequences for known genetic polymorphisms, was run across all 792 samples using the mtbc test suite and default parameters. […]

PMCID: 4264550
PMID: 25476850
DOI: 10.1186/s12866-014-0307-2

[…] from goroka exhibits a special spoligotyping pattern with only spacers 40–43 being present (sample no. 4 in figure ). that spoligotyping pattern has been confirmed with in silico spoligotyping using kvarq []. per standard definition, this would define that strain as belonging to the beijing family of lineage 2 [,]. however, snp-typing assigned this strain to lineage 1, therefore representing […]


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KvarQ institution(s)
Swiss Tropical and Public Health Institute, Basel, Switzerland

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