recipe mindthegap

MindTheGap performs detection and assembly of DNA insertion variants in NGS read datasets with respect to a reference genome. MindTheGap can also be used as a genome assembly finishing tool, it can fill the gaps between a set of input contigs without any a priori on their relative order and orientation.







biotools: mindthegap, doi: 10.1093/bioinformatics/btu545

package mindthegap

(downloads) docker_mindthegap



depends libgcc-ng:


depends libstdcxx-ng:


depends libzlib:


depends zlib:



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 mindthegap

and update with::

   mamba update mindthegap

To create a new environment, run:

mamba create --name myenvname mindthegap

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

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