Synk - Rapid synteny plotting tool using Compleasm outputs
Synk is a tool to plot synteny using BUSCO genes. With BUSCO genes, synteny is plotted rapidly and avoids the issue of mapping paralogs, sinch BUSCO genes are conserved, single copy orthologs. This makes Synk an effective tool for analysing synteny between distantly related species.
Synk is a python script. Download it!
git clone https://github.com/jomhoff/Synk.git
cd Synk
Dependencies: Pandas; Matplotlib; Rideogram
Usage example:
python synk.py \
--karyotype1 pfas_karyotype.txt \
--karyotype2 tiliqua_karyotype.txt \
--busco1 pfas_busco_format.tsv \
--busco2 tiliqua_busco_format.tsv \
--rep1 replacement_pfas.txt \
--rep2 replacement_tiliqua.txt \
--outdir output_directory \
--cmap viridis \
--plot
Required inputs:
--karyotype1 First species karyotype file (must have columns: Chr, Start, End, Species)
--karyotype2 Second species karyotype file (same format as above)
--busco1 BUSCO full table from species 1 (full_table_BUSCO.tsv)
--busco2 BUSCO full table from species 2
--rep1 Replacement map for species 1 chromosome names (ie. chr1 1)
--rep2 Replacement map for species 2 chromosome names
--outdir Directory for output files
Optional inputs:
--cmap Colormap for chromosome gradient (default: plasma; other: viridis, magma)
--plot Include this flag to generate an ideogram PNG/SVG with RIdeogram
--rscript_path Path to output R script (default: plot_ideogram.R)
--karyo_size Label text size (default: 5)
--karyo_color Label text color (default: black)
Output Files:
- chr_color_map.txt : Map of chromosome names to colors
- color_replace.txt : Map of numeric chromosome order to colors
- merged_busco.txt : Merged BUSCO hits shared between both species
- final_synteny.txt : Synteny links colored by species 1 chromosome
- dual_karyotype.txt : Combined karyotype file with label and fill info
- chromosome.png/.svg : RIdeogram synteny plot (if --plot is used)
If you use Synk in your work, please cite:
Hoffman, J.J., Burbrink, F.T., Pyron, R.A., Raxworthy, C.J., 2025. Telomere-to-telomere reference genome of the common five-lined skink, Plestiodon fasciatus (Squamata: Scincidae). https://doi.org/10.1101/2025.07.03.663019