A tool to visualise synteny relationships between genomes.
Installation
conda create synteny_plotter
conda activate synteny_plotter
conda install conda-forge::r-dplyr
conda install -c conda-forge r-argparse
Testing run
Rscript scripts/generate_synteny_plot.R -busco1 test_data/Melitaea_cinxia.tsv -busco2 test_data/Vanessa_cardui.tsv -chrom1 test_data/Melitaea_cinxia_info.tsv -chrom2 test_data/Vanessa_cardui_info.tsv -o test_data/test
The following reads testing files, produces order of chromosomes for Vanessa (test_data/Vanessa_cardui_info_generated.tsv)
Rscript scripts/dev_generate_chromosome_file.R
Now I would like to compare the manual and generated versions
Rscript scripts/generate_synteny_plot.R -busco1 test_data/Melitaea_cinxia.tsv -busco2 test_data/Vanessa_cardui.tsv -chrom1 test_data/Melitaea_cinxia_info.tsv -chrom2 test_data/Vanessa_cardui_curated_info.tsv -o test_data/test_curated
Rscript scripts/generate_synteny_plot.R -busco1 test_data/Melitaea_cinxia.tsv -busco2 test_data/Vanessa_cardui.tsv -chrom1 test_data/Melitaea_cinxia_info.tsv -chrom2 test_data/Vanessa_cardui_info_generated.tsv -o test_data/test_generated
The order seems to work well.