recipe hapsolo

An optimization approach for removing secondary haplotigs during diploid genome assembly and scaffolding.



GPL / GPL-2.0



package hapsolo

(downloads) docker_hapsolo



depends augustus:

depends blast:

depends blat:


depends braker:

depends busco:


depends matplotlib-base:


depends minimap2:

depends mummer:

depends pandas:

depends parallel:

depends python:


depends quast:

depends ucsc-fatotwobit:



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 hapsolo

and update with::

   mamba update hapsolo

To create a new environment, run:

mamba create --name myenvname hapsolo

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

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