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.
Some example testsuites can be found in the testsuites/ subdirectory.
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) can be downloaded from the Swiss TPH website.
For more information refer to the online documentation.
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. http://www.swisstph.ch/kvarq.