:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'unimap' .. highlight: bash unimap ====== .. conda:recipe:: unimap :replaces_section_title: :noindex: Unimap is a fork of minimap2 optimized for assembly\-to\-reference alignment. :homepage: https://github.com/lh3/unimap :license: MIT :recipe: /`unimap `_/`meta.yaml `_ Unimap is a fork of minimap2 optimized for assembly\-to\-reference alignment. It integrates the minigraph chaining algorithm and can align through long INDELs \(up to 100kb by default\) much faster than minimap2. Unimap is a better fit for resolving segmental duplications and is recommended over minimap2 for alignment between high\-quality assemblies. Unimap does not replace minimap2 for other types of alignment. It drops the support of multi\-part index and short\-read mapping. Its long\-read alignment is different from minimap2 but is not necessarily better. Unimap is more of a specialized minimap2 at the moment. .. conda:package:: unimap |downloads_unimap| |docker_unimap| :versions: ``0.1-4``,  ``0.1-3``,  ``0.1-2``,  ``0.1-1``,  ``0.1-0`` :depends libgcc-ng: ``>=12`` :depends libzlib: ``>=1.2.13,<1.3.0a0`` :requirements: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`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 unimap and update with:: mamba update unimap To create a new environment, run:: mamba create --name myenvname unimap 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 quay.io/biocontainers/unimap: (see `unimap/tags`_ for valid values for ````) .. |downloads_unimap| image:: https://img.shields.io/conda/dn/bioconda/unimap.svg?style=flat :target: https://anaconda.org/bioconda/unimap :alt: (downloads) .. |docker_unimap| image:: https://quay.io/repository/biocontainers/unimap/status :target: https://quay.io/repository/biocontainers/unimap .. _`unimap/tags`: https://quay.io/repository/biocontainers/unimap?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| badge with the following MarkDown:: [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/unimap/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/unimap/README.html