odgi viz, display for whole chromosomes

pangenome / odgi

Optimized Dynamic Genome/Graph Implementation: understanding pangenome graphs

https://doi.org/10.1093/bioinformatics/btac308

MIT License

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odgi viz, display for whole chromosomes #542

Closed Rktf closed 10 months ago

Rktf commented 10 months ago

Greetings,

I want to display 10 genomes alignment with odgi. 1 of those genomes contains 36 chromosomes. When using odgi viz, I got 1 chromosome by row. i.e, I got many raws for genome sequence n°1, many rows for genome sequence n°2, etc... Capture

Is there any possibility to display whole genome with all the chromosome for each line? i.e, 1 whole genome per line inside the png outputed by odgi.

Many thanks in advance

AndreaGuarracino commented 10 months ago

Yes, it is possible!

odgi paths -i your_graph.og -L | cut -f 1,2 | sort | uniq > your_prefixes.txt
odgi viz -i your_graph.og -o your_visualization.png -M your_prefixes.txt

Rktf commented 10 months ago

@AndreaGuarracino Many thanks for your answer. It helps me