:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'minialign' .. highlight: bash minialign ========= .. conda:recipe:: minialign :replaces_section_title: :noindex: Fast and accurate alignment tool for PacBio and Nanopore long reads. :homepage: https://github.com/ocxtal/minialign :license: MIT :recipe: /`minialign `_/`meta.yaml `_ Minialign is a little bit fast and moderately accurate nucleotide sequence alignment tool designed for PacBio and Nanopore long reads. It is built on three key algorithms\, minimizer\-based index of the minimap overlapper\, array\-based seed chaining\, and SIMD\-parallel Smith\-Waterman\-Gotoh extension. .. conda:package:: minialign |downloads_minialign| |docker_minialign| :versions: ``0.5.3-2``,  ``0.5.3-1``,  ``0.5.3-0``,  ``0.5.2-0``,  ``0.4.2-1``,  ``0.4.2-0``,  ``0.4.0-0``,  ``0.3.1-0`` :depends zlib: ``>=1.2.11,<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 minialign and update with:: mamba update minialign To create a new environment, run:: mamba create --name myenvname minialign 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/minialign: (see `minialign/tags`_ for valid values for ````) .. |downloads_minialign| image:: https://img.shields.io/conda/dn/bioconda/minialign.svg?style=flat :target: https://anaconda.org/bioconda/minialign :alt: (downloads) .. |docker_minialign| image:: https://quay.io/repository/biocontainers/minialign/status :target: https://quay.io/repository/biocontainers/minialign .. _`minialign/tags`: https://quay.io/repository/biocontainers/minialign?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/minialign/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/minialign/README.html