Organisms and Cytobands

Built-in Organisms

PangyPlot has built-in cytobands for the following:

	Organism	Build
🧍	human-hg38 [default]	hg38
🧍	human-t2t	chm13
🐁	mouse	mm39
🪰	fruitfly	dm6
🐠	zebrafish	danRer11
🐓	chicken	galGal6
🐇	rabbit	oryCun2
🐕	dog	canFam3
❓	custom
❌	none

Note

More organisms can be added on request, if you have cytoband files. Please open an issue on the GitHub repository.

If your organism is not in this list, you can either generate a dummy cytoband from your reference FASTA, or run without one.

Custom Organisms

To add a custom organism, you need to provide two files:

A cytoband file, tab-separated with five columns and no header (chrom, start, end, band name, stain)
A text file specifying the main canonical chromosomes (one per line)

chr1 0       2300000 p36.33  gneg
chr1 2300000 5300000 p36.32  gpos25

chr1
chr2

Once these files are prepared, you can specify them during the interactive setup process, which sets ORGANISM=custom along with CYTOBAND_PATH and CANONICAL_PATH.

Examples can be found in pangyplot/static/cytoband.

Dummy Cytobands

For organisms with no cytogenetic data, PangyPlot can generate a dummy pair of the files above from a reference FASTA index (.fai). Each chromosome is drawn as a single bar spanning its length.

samtools faidx myorganism.fa
pangyplot cytoband --fai myorganism.fa.fai --out-dir cytoband/ --genome myOrg

This writes cytoband/myOrg.cytoBand.txt and cytoband/myOrg.canonical.txt, and prints the lines to add to your .env:

ORGANISM=custom
CYTOBAND_PATH=/abs/path/cytoband/myOrg.cytoBand.txt
CANONICAL_PATH=/abs/path/cytoband/myOrg.canonical.txt

The chromosome view then renders as it does for a built-in organism.

Note

Sequences shorter than 1 Mb are left out, since a .fai usually lists many unplaced scaffolds. Use --min-length, --pattern or --chromosomes to choose which sequences appear.

See pangyplot cytoband for the full set of options.

Running Without a Cytoband

Setting ORGANISM=none runs PangyPlot with no cytoband data. The chromosome and locus selectors are hidden, and you navigate by typing a region into the coordinate box (chr:start-end).