Metadata-Version: 2.1
Name: mummer-idotplot
Version: 0.1.3
Summary: Generate interactive dotplot from MUMmer4 output using plotly
Home-page: https://github.com/ryought/mummer-idotplot
Author: ryought
Author-email: ryonakabayashi@gmail.com
License: MIT
Description: # mummer-idotplot
        Generate interactive dotplot from MUMmer4 output using plotly
        
        ## 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
        ```
        
        
Platform: UNKNOWN
Description-Content-Type: text/markdown
