Support Microsynteny plots with genome alignment data

Adamtaranto commented 1 year ago

jcvi.graphics.ribbon module is a modified version of the synteny module which allows plotting of arbitrary alignments and multiple genomic feature tracks. Ribbon plots are not based on ortholog linkages but instead on whole genome alignments.

This issue is for tracking progress on the ribbon module in preparation for merging it into the main project.

[ ] Modify LASTZ wrapper to do pairwise alignments between a defined set of contigs
[ ] Add filter for alignment length and quality
[ ] Convert LASTZ output to .bed and .blocks files with wga2ribbon app
[ ] Extend wga2ribbon to use Minimap2 asm2asm alignment format
[ ] Modify synteny module to plot arbitrary alignments
[ ] Add logging and comment new functions
[ ] Check that we are using pre-existing jcvi functions where possible
[ ] Document use cases in new wiki page

AlbertoBernacchi commented 7 months ago

Hello Adamataranto, have you managed to modify the synteny module to plot arbitrary alignments? Can you point me to a bioinformatic package that is able to do so? I'm currently searching for it but with no luck. Thank you.

Adamtaranto commented 7 months ago

I have a development branch that works for this. It is currently undocumented and you will need to provide your own alignments.

I can provide some support if you want to give it a go.

AlbertoBernacchi commented 7 months ago

Hi Adamtarando, thank you for the quick response. I'll try to explain what I want to do and what I can currently do with the data I have. I have two mitochondrial genomes of which I want to analyze the collinearity. However, I have yet to find a tool that allows for the analysis of non-coding regions. Currently I have the .bed files, .gff, .fasta and .blast of both mitochondrial genomes. Thank you again for your help.

tanghaibao / jcvi

Support Microsynteny plots with genome alignment data #547