A somewhat updated and more portable version of Thomas Hackl's minidot. I've dropped the bash wrapper in favour of a Pythony one to improve support on Mac and make it a little more straightforward to use. Additionally, I've added a few extra plotting options and updated the R script to use the PAF dv tag as the sequence identity, which means it works with minimap2 instead.

• minimap2 (specify --mapper path/to/minimap2 if not on your $PATH)
• python with pysam
• R-base with ggplot2, stringr, scales, argparse

git clone https://github.com/samstudio8/minidot.git

python minidot/minidot.py minidot/minidot.R output.png seq1.fa seq2.fa [seq3.fa ...]

minidot will merge all sequences in each FASTA, using the first sequence name as the canonical sequence name. You can naively suppress sequences based on their name with --drop-contains. minimap2 will align every pairing of the new merged FASTAs to construct a PAF, which is then plotted as a diagonal plot by minidot.R.

Patches welcome, but this was a best-effort revival of an older project.