recipe haphpipe

HAplotype and PHylodynamics pipeline for viral assembly, population genetics, and phylodynamics.




GPL License



package haphpipe

(downloads) docker_haphpipe



depends biopython:

depends blast:

depends bowtie2:

depends bwa:

depends flash:

depends freebayes:

depends future:

depends gatk:


depends gsutil:

depends mafft:

depends modeltest-ng:

depends mummer:

depends picard:

depends python:


depends pyyaml:

depends raxml-ng:

depends samtools:


depends seqtk:

depends sierrapy:

depends spades:

depends sra-tools:

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 haphpipe

and update with::

   mamba update haphpipe

To create a new environment, run:

mamba create --name myenvname haphpipe

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

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