https://github.com/fmalmeida/plot_nucmer
A simple script to run an alignment with nucmer and visualise its results.
https://github.com/fmalmeida/plot_nucmer
circular-visualization conda ggbio nucmer plot r whole-genome-alignment
Last synced: 5 months ago
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A simple script to run an alignment with nucmer and visualise its results.
- Host: GitHub
- URL: https://github.com/fmalmeida/plot_nucmer
- Owner: fmalmeida
- License: gpl-3.0
- Created: 2021-07-14T12:54:41.000Z (almost 5 years ago)
- Default Branch: main
- Last Pushed: 2023-04-17T18:06:26.000Z (about 3 years ago)
- Last Synced: 2023-10-20T19:52:30.796Z (over 2 years ago)
- Topics: circular-visualization, conda, ggbio, nucmer, plot, r, whole-genome-alignment
- Language: Shell
- Homepage: https://plot-nucmer.readthedocs.io/en/latest/
- Size: 553 KB
- Stars: 4
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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# Plot nucmer
plot_nucmer is a simple script to run an alignment with nucmer and visualise its results.
## Table of contents
* [Features](https://github.com/fmalmeida/plot_nucmer#features)
* [Installation](https://github.com/fmalmeida/plot_nucmer#installation)
* [Documentation](https://github.com/fmalmeida/plot_nucmer#documentation)
* [How can you colaborate?](https://github.com/fmalmeida/plot_nucmer#collaborating)
* [Citation](https://github.com/fmalmeida/plot_nucmer#citation)
## Features
This script is designed to:
* Perform whole genome alignment between FASTAs with [nucmer](https://github.com/mummer4/mummer).
* Filter alignments by length and identity
* Plot these alignments in circular visualisation with [ggbio](https://bioconductor.org/packages/release/bioc/html/ggbio.html).
It is an automation of the methods described by Taylor Reiter at https://taylorreiter.github.io/2019-05-11-Visualizing-NUCmer-Output/.
> 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.
## Installation
## Conda package
> Users are advised to create separate conda environments
```bash
# Get the conda package
mamba create -n plot_nucmer -c conda-forge -c bioconda -c falmeida plot_nucmer
```
:fire: Users are advised to use [mamba](https://github.com/mamba-org/mamba) since it is faster.
## Docker image
```bash
# pull and enter the image
docker run --platform linux/amd64 -v $(pwd):/work -w /work -it fmalmeida/plot_nucmer
# run the script from inside the container
root@c896e9370a2f:/work# plot_nucmer --help
```
> Remember to use the parameters `-v` so your files are available to the docker container.
: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.
## Documentation
Command line documentation can be seen with:
```bash
# activate env
conda activate plot_nucmer
# see help
plot_nucmer --help
```
Additionally, an online documentation and a simple step-by-step quickstart is provided:
* [Online manual >>](https://plot-nucmer.readthedocs.io/en/latest/)
* [Step-by-step quickstart >>](https://plot-nucmer.readthedocs.io/en/latest/quickstart.html)
## Collaborating
You can collaborate by:
* flagging an **enhancement issue** discussing your idea in the homepage of the project
* you can fork the repo, create and start the implementation of your own script/command in the project and then submit a **pull request**
* 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.
* Of course, you will be recognized as the developer/creator of that specific implementation.
Checkout more at about forking and contributing to repos at:
* [Chase's tutorial](https://gist.github.com/Chaser324/ce0505fbed06b947d962)
* [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)
## Citation
To 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.