recipe nullarbor

Reads to report pipeline for bacterial isolate NGS data






package nullarbor

(downloads) docker_nullarbor



depends abricate:


depends any2fasta:


depends centrifuge:


depends fasttree:


depends iqtree:


depends kraken:


depends kraken2:


depends make:


depends mash:


depends megahit:


depends mlst:


depends newick_utils:


depends perl:


depends perl-bioperl:


depends perl-file-spec:

depends perl-file-which:

depends perl-findbin:

depends perl-json:

depends perl-list-moreutils:


depends perl-path-tiny:

depends perl-svg:

depends perl-text-csv:

depends perl-time-piece:

depends perl-yaml-tiny:

depends pigz:

depends prokka:


depends quicktree:


depends roary:


depends samtools:


depends seqtk:


depends shovill:


depends skesa:


depends snippy:


depends snp-dists:


depends snpeff:


depends spades:


depends trimmomatic:




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 nullarbor

and update with::

   mamba update nullarbor

To create a new environment, run:

mamba create --name myenvname nullarbor

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 `nullarbor/tags`_ for valid values for ``<tag>``)

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