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Protocols

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

Versioning


No version available

Publication for KvarQ

KvarQ citations

 (6)
call_split

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

2017
PLoS One
PMCID: 5604961
PMID: 28926571
DOI: 10.1371/journal.pone.0184510
call_split See protocol

[…] 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 […]

library_books

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

2017
Antimicrob Agents Chemother
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 […]

library_books

Mycobacterium tuberculosis Lineage 4 comprises globally distributed and geographically restricted sublineages

2016
Nat Genet
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, […]

library_books

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

2016
PLoS One
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 […]

library_books

Rapid determination of anti tuberculosis drug resistance from whole genome sequences

2015
Genome Med
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. […]

library_books

Diversity of Mycobacterium tuberculosis and drug resistance in different provinces of Papua New Guinea

2014
BMC Microbiol
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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