recipe shovill-se

An fork of Shovill (microbial assembly pipeline for Illumina paired-end reads) that supports single-end reads.






package shovill-se

(downloads) docker_shovill-se



depends bwa:


depends flash:


depends kmc:


depends lighter:


depends megahit:


depends perl:

depends perl-file-spec:

depends perl-findbin:

depends pigz:

depends pilon:


depends samclip:


depends samtools:


depends seqtk:


depends skesa:


depends spades:


depends trimmomatic:


depends velvet:




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 shovill-se

and update with::

   mamba update shovill-se

To create a new environment, run:

mamba create --name myenvname shovill-se

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 `shovill-se/tags`_ for valid values for ``<tag>``)

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