A set of scripts and tools for the analysis of viral NGS data

Versions 1.10.1, 1.11.0, 1.12.0, 1.12.1, 1.12.2, 1.13.2, 1.13.3, 1.13.4, 1.5.4, 1.5.5, 1.6.0, 1.6.1, 1.7.0, 1.7.1, 1.8.0, 1.9.0, 1.9.1, 1.9.2


With an activated Bioconda channel (see 2. Set up channels), install with:

conda install viral-ngs

and update with:

conda update viral-ngs


This package makes use of GATK. Due to license restrictions, this recipe cannot distribute and install GATK directly as a dependency. To fully install GATK, you must download a licensed copy of GATK from the Broad Institute ( ), install this package (which will install the GATK wrapper package), and call “gatk-register /path/to/GenomeAnalysisTK[-$PKG_VERSION.tar.bz2|.jar]”, which will copy GATK into your conda environment. This package also makes use of Novoalign, which can be installed successfully as a conda package, however the unlicensed version of Novoalign runs in single-threaded mode. To enable multithreaded operation, it is necessary to supply a “novoalign.lic” license file and call “novoalign-license-register” to copy the license file into the conda environment.


A Docker container is available at