recipe assemblytics

analyze a genome assembly by comparing it to a reference genome






Assemblytics detects and analyzes variants from a de novo genome assembly aligned to a reference genome. It incorporates a unique anchor filtering approach to increase robustness to repetitive elements and identifies six classes of variants based on their distinct alignment signatures. Assemblytics can be applied both to comparing aberrant genomes, such as human cancers, to a reference, or to identify differences between related species.

package assemblytics

(downloads) docker_assemblytics



depends mummer:

depends numpy:

depends python:

depends r-base:

depends r-ggplot2:

depends r-plyr:

depends r-rcolorbrewer:

depends r-scales:



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 assemblytics

and update with::

   mamba update assemblytics

To create a new environment, run:

mamba create --name myenvname assemblytics

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

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