svgenes

This program finds syntenic regions between two genomes, using genome annotations instead of aligning sequences. It maps confident inversions and translocations, plots them, and writes them to BED files, also writing lists of genes in inverted and translocated regions.

Outputs

• BED file listing syntenic blocks on genome1 -> genome2, including orientation
• BED file listing syntenic blocks on genome2 -> genome1, including orientation
• List of genes present in inverted regions
• List of genes present in translocated regions
• Plot showing synteny between genomes (and identified inverted/translocated regions)

Installation

conda env create --file=svgenes.yml

Running

./svgenes.py --anno1 [gtf/gff3 file 1] \
    --anno2 [gtf/gff3 file 2] \
    --fai1 [FAI file for species 1] \
    --fai2 [FAI file for species 2] \
    --species1 [name of species 1] \
    --species2 [name of species 2] \
    --output [output file prefix ]