DiscoPlot

Visualising discordant reads.

Quickstart
Tutorial 1 - Exploring a mock genome (coming soon)
Tutorial 2 - Exploring a requenced genome (coming soon)

Quick Start - paired-end/mate-pair short reads.

Align reads with your favourite short read aligner (e.g. BWA, Bowtie2)
Create DiscoPlot from sam file with 5000 bins - open in a matplotlib window: 

 DiscoPlot.py -sam sam_file.sam -s 5000
Create a DiscoPlot from a bam file using a bin size of 10,000bp - save as .png file: 
 DisocPlot.py -bam bam_file.bam -bin 10000 -o discoplot.png

Quick Start - long reads

To automatically generate a BLAST alignment using BLAST+ run 
 DiscoPlot.py -r reads.fa -ref reference.fasta -B -s 5000
To provide DiscoPlot with an alignment file (BLAST tab delimited format) 
 DiscoPlot -ref reference.fasta -b alignment.out -s 5000

For more in depth description of functionality and work flows please see the manual.

Contact: mjsull@gmail.com

More tutorials coming soon