recipe snippy

Rapid bacterial SNP calling and core genome alignments



GPL / GPL-2.0




biotools: snippy, usegalaxy-eu: snippy

package snippy

(downloads) docker_snippy



depends any2fasta:


depends bcftools:


depends bedtools:


depends bwa:


depends freebayes:


depends minimap2:


depends openjdk:


depends parallel:


depends perl:

depends perl-bioperl:


depends samclip:


depends samtools:


depends seqtk:


depends snp-sites:


depends snpeff:


depends vcflib:


depends vt:




You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install snippy

and update with::

   mamba update snippy

To create a new environment, run:

mamba create --name myenvname snippy

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `snippy/tags`_ for valid values for ``<tag>``)

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