ryought/mummer-idotplot

Generate interactive dotplot from mummer4 output using plotly

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

mummer-idotplot's Issues

How can I plot all the contigs？

My query have at least 100 contigs，So What I should set the parameter to plot all the contigs easily？

mummer-idotplot 24771.mum 24771.html --refs all --querys all

like this?
Could U plz give me a answer?Thanks!