R package to draw synteny plots in three different styles

This package has been developed by Joana Damas ([email protected]) and Marta Farré ([email protected])

devtools::install_github("marta-fb/syntenyPlotteR")

Please provide a file with the synteny blocks information, following this format, separated by tabs.

DO NOT include a header line

• chr - chromosome of reference species -- it ONLY accepts numbers
• start - start of block in reference species
• end - end of block in reference species
• tarChr - chromosome of target species
• tarSt - start of block in target species
• tarEnd - end of block in target species
• orient - orientation of the block (1 or -1)
• tarSpecies - name of the target species

draw.eh("input file","output file name",chromosomeRange)

• outputName - name of output file
• chromosomeRange - range of chromosome numbers in reference species.

library(syntenyPlotteR)

draw.eh("syntenicBlocks_oneChromosome_severalSps.txt","testOut",1:1)

library(syntenyPlotteR)
draw.ideogram("syntenicBlocks.txt", "reference_chr_size", "target_chr_size")

• reference_chr_size Lenghts of reference chromosomes, scaffolds or contigs. Format: ID Length
• target_chr_size Lenghts of target chromosomes, scaffolds or contigs. Format: ID Length

library(syntenyPlotteR)
draw.pairwise("syntenicBlocks.txt", "outputFileName", "reference_chr_size", "target_chr_size", "refName", "tarName")

• outputFilename: Name of the output file
• target_chr_size: Lenghts of target chromosomes, scaffolds or contigs. Format: ID Length
• reference_chr_size: Lenghts of reference chromosomes, scaffolds or contigs. Format: ID Length
• refName: name of the reference genome
• tarName: name of the target genome

1. Update vignette
2. Preprint in Biorxiv

While we're preparing the publication, please cite:
Farré M, Kim J, et al. Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks. Genome Research 2019 Apr;29(4):576-589