Targeted and Direct Variant Calling in FastQ Reads of Bacterial Genomes

The program KvarQ performs rapid in silico genotyping for selected loci (e.g. phylogenetic SNPs, drug resistance mutations) in bacterial genome sequences in FastQ format. Mapping to a whole-genome reference sequence or de novo assembly or the short reads is not necessary.

Testsuites for different target polymorphisms can be configured or imported. In the downloadable package, KvarQ contains testsuites for MTBC phylogenetic lineage classification, MTBC drug resistance identification and spoligotyping (the latter adapted and modified from SpolPred).


KvarQ is written in Python and C, is open-source and published under GNU GPLv3.

Pre-compiled packages are available for Windows 7 or later, and for Mac OS X (10.6 or later). For Mac OS X 10.9 (Mavericks), please allow installation of additional software as described here.

KvarQ is available as source-code under https://github.com/kvarq/kvarq.


The documentation including the installation procedure is found under http://kvarq.readthedocs.org.

How to cite

KvarQ: targeted and direct variant calling from fastq reads of bacterial genomes. Steiner A, Stucki D, Coscolla M, Borrell S, Gagneux S. BMC Genomics. 2014 Oct 9;15(1):881. doi:10.1186/1471-2164-15-881. www.swisstph.ch/kvarq.