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returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["circular-visualization","conda","ggbio","nucmer","plot","r","whole-genome-alignment"],"created_at":"2026-01-22T21:55:39.259Z","updated_at":"2026-01-22T21:55:39.861Z","avatar_url":"https://github.com/fmalmeida.png","language":"Shell","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![GitHub release (latest by date)](https://img.shields.io/github/v/release/fmalmeida/plot_nucmer?style=flat-square)](https://github.com/fmalmeida/plot_nucmer/releases) [![](https://anaconda.org/falmeida/plot_nucmer/badges/version.svg)](https://anaconda.org/falmeida/plot_nucmer/badges) [![](https://anaconda.org/falmeida/plot_nucmer/badges/latest_release_date.svg)](https://anaconda.org/falmeida/plot_nucmer/badges) [![](https://anaconda.org/falmeida/plot_nucmer/badges/platforms.svg)](https://anaconda.org/falmeida/plot_nucmer) [![](https://anaconda.org/falmeida/plot_nucmer/badges/installer/conda.svg)](https://anaconda.org/falmeida/plot_nucmer)\n\n# Plot nucmer\n\nplot_nucmer is a simple script to run an alignment with nucmer and visualise its results.\n\n## Table of contents\n\n* [Features](https://github.com/fmalmeida/plot_nucmer#features)\n* [Installation](https://github.com/fmalmeida/plot_nucmer#installation)\n* [Documentation](https://github.com/fmalmeida/plot_nucmer#documentation)\n* [How can you colaborate?](https://github.com/fmalmeida/plot_nucmer#collaborating)\n* [Citation](https://github.com/fmalmeida/plot_nucmer#citation)\n\n## Features\n\nThis script is designed to:\n\n* Perform whole genome alignment between FASTAs with [nucmer](https://github.com/mummer4/mummer).\n* Filter alignments by length and identity\n* Plot these alignments in circular visualisation with [ggbio](https://bioconductor.org/packages/release/bioc/html/ggbio.html).\n\nIt is an automation of the methods described by Taylor Reiter at https://taylorreiter.github.io/2019-05-11-Visualizing-NUCmer-Output/.\n\n\u003e If you don't like very much the combination of nucmer and ggbio, check out my other package called [easy_circos](https://github.com/fmalmeida/easy_circos) that uses blastn and circos.\n\n## Installation\n\n## Conda package\n\n\u003e Users are advised to create separate conda environments\n\n```bash\n# Get the conda package\nmamba create -n plot_nucmer -c conda-forge -c bioconda -c falmeida plot_nucmer\n```\n\n:fire: Users are advised to use [mamba](https://github.com/mamba-org/mamba) since it is faster.\n\n## Docker image\n\n```bash\n# pull and enter the image\ndocker run --platform linux/amd64 -v $(pwd):/work -w /work -it fmalmeida/plot_nucmer\n\n# run the script from inside the container\nroot@c896e9370a2f:/work# plot_nucmer --help\n```\n\n\u003e Remember to use the parameters `-v` so your files are available to the docker container.\n\n:fire: The \"--platform linux/amd64\" only tells docker the architecture that the image was built so it emulates the correct one. You can run this exact command in any system architecture.\n\n## Documentation\n\nCommand line documentation can be seen with:\n\n```bash\n# activate env\nconda activate plot_nucmer\n\n# see help\nplot_nucmer --help\n```\n\nAdditionally, an online documentation and a simple step-by-step quickstart is provided:\n\n* [Online manual \u003e\u003e](https://plot-nucmer.readthedocs.io/en/latest/)\n* [Step-by-step quickstart \u003e\u003e](https://plot-nucmer.readthedocs.io/en/latest/quickstart.html)\n\n## Collaborating\n\nYou can collaborate by:\n\n* flagging an **enhancement issue** discussing your idea in the homepage of the project\n* you can fork the repo, create and start the implementation of your own script/command in the project and then submit a **pull request**\n    * I'll then check the request, make sure it is in the same format and standards of the already implemented commands and **confirm** the inclusion.\n    * Of course, you will be recognized as the developer/creator of that specific implementation.\n\nCheckout more at about forking and contributing to repos at:\n\n* [Chase's tutorial](https://gist.github.com/Chaser324/ce0505fbed06b947d962)\n* [github's advises on how to collaborate to projects](https://docs.github.com/en/free-pro-team@latest/github/collaborating-with-issues-and-pull-requests)\n\n## Citation\n\nTo cite this pipeline users can use the github url. Users are encouraged to cite the python packages used in this pipeline whenever their outputs are valuable.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffmalmeida%2Fplot_nucmer","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ffmalmeida%2Fplot_nucmer","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffmalmeida%2Fplot_nucmer/lists"}