https://github.com/dfguan/cgplot

comparative genome dot plot viewer
https://github.com/dfguan/cgplot

Last synced: 4 months ago
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comparative genome dot plot viewer

• Host: GitHub
• URL: https://github.com/dfguan/cgplot
• Owner: dfguan
• License: mit
• Created: 2018-05-14T08:48:40.000Z (about 6 years ago)
• Default Branch: master
• Last Pushed: 2019-05-19T20:09:21.000Z (about 5 years ago)
• Last Synced: 2024-01-17T01:00:55.792Z (6 months ago)
• Language: Python
• Size: 3.29 MB
• Stars: 8
• Watchers: 2
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Lists

• repo-5916-awesome-genome-visualization - cgplot - genome-visualization/cgplot.png) (Static)
• awesome-genome-visualization - cgplot

README

        
# cgplot

a script for viewing sequence aligments and read-depth

## Dependency

1. python3 

## Quick Start 

```

python cgplot.py -c 3L:23000000-28000000 -q000050F_arrow_arrow,000057F_arrow_arrow,000021F_arrow_arrow tests/Anoph_coluzzii2chrom.paf tests/PB.cov.wig

```

This will generate a image showing how the query contigs 50F, 57F and 21F are mapped to 23M-28M region of chromsome 3L, and also read depth plot for the contigs are shown on the bottom. 

![plot.png](https://github.com/dfguan/cgplot/blob/master/tests/plot.png) 

## Synopsis

```

usage: cgplot.py [options] paf_file wig_file

Genome Comparison plot

positional arguments:

  paf_file              a paf file

  wig_file              a wig file, set window size 1024

optional arguments:

  -h, --help            show this help message and exit

  -c                    chromsome region in chr:start-end or chr format

  -q                    query name(s) mapped into the chromsome region,add comma to join multiple query names, support a maximum of 5 contigs

  -l                    minimum mapped length

  -o                    output file

  -t                    figure title

  --version             show program's version number and exit

```