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KvarQ specifications


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


No version available

Publication for KvarQ

KvarQ citations


Whole genome sequencing illuminates the evolution and spread of multidrug resistant tuberculosis in Southwest Nigeria

PLoS One
PMCID: 5604961
PMID: 28926571
DOI: 10.1371/journal.pone.0184510
call_split See protocol

[…] from 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 more high […]


Some Synonymous and Nonsynonymous gyrA Mutations in Mycobacterium tuberculosis Lead to Systematic False Positive Fluoroquinolone Resistance Results with the Hain GenoType MTBDRsl Assays

Antimicrob Agents Chemother
PMCID: 5365657
PMID: 28137812
DOI: 10.1128/AAC.02169-16

[…] ance 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 of these tools […]


Mycobacterium tuberculosis Lineage 4 comprises globally distributed and geographically restricted sublineages

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

[…] s assessed by manually inspecting BAM alignment files from BWA mappings in Artemis for the presence of reads at the genomic regions with described deletions. Alternatively, we used a new testsuite in KvarQ to check for reads aligning to 25 bp query sequences of the corresponding deletion. […]


Whole Genome Sequencing Analysis of Serially Isolated Multi Drug and Extensively Drug Resistant Mycobacterium tuberculosis from Thai Patients

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

[…] 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 p […]


Rapid determination of anti tuberculosis drug resistance from whole genome sequences

Genome Med
PMCID: 4446134
PMID: 26019726
DOI: 10.1186/s13073-015-0164-0
call_split See protocol

[…] e 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. Sen […]


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

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