Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
https://github.com/ryought/mummer-idotplot
Generate interactive dotplot from mummer4 output using plotly
https://github.com/ryought/mummer-idotplot
bioinformatics dotplot genome-alignment mummer visualization
Last synced: 4 months ago
JSON representation
Generate interactive dotplot from mummer4 output using plotly
- Host: GitHub
- URL: https://github.com/ryought/mummer-idotplot
- Owner: ryought
- Created: 2019-05-22T10:23:09.000Z (about 5 years ago)
- Default Branch: master
- Last Pushed: 2020-02-29T07:41:10.000Z (over 4 years ago)
- Last Synced: 2024-02-26T13:23:09.639Z (4 months ago)
- Topics: bioinformatics, dotplot, genome-alignment, mummer, visualization
- Language: Python
- Homepage:
- Size: 10.7 KB
- Stars: 25
- Watchers: 2
- Forks: 5
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
Lists
- repo-5916-awesome-genome-visualization - Mummer-idotplot
- awesome-genome-visualization - Mummer-idotplot
README
# mummer-idotplot
Generate interactive dotplot from MUMmer4 output using plotly
[](https://pepy.tech/project/mummer-idotplot)
[](https://badge.fury.io/py/mummer-idotplot)
## Installation
```
$ pip install mummer-idotplot
```
`plotly` is required to install.
## Usage
When aligning two sequences with MUMmer4, you should set an option `-F`(force 4 column output format) and `-L`(show length of query). Also, you should not use `-c` option, which change output position of match starting position and have bugs.
So for example:
If you have `chr1, chr2` in `reference.fasta`, and `contig1, contig2` in `query.fasta`
```
$ mummer -maxmatch -F -L -b -l 10 reference.fasta query.fasta > output.mum
$ mummer-idotplot output.mum output.html --ref chr1 chr2 --query contig1 contig2
$ mummer-idotplot output.mum output.html --ref chr1:0:50000 chr2:100:20000 --query contig1 contig2 # you can specify the region to plot
$ open output.html # you'll see dotplot in your browser
```