SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies

Here, we present SyRI, an efficient tool for genome-wide structural rearrangement identification from genome graphs, which are build up from pair-wise whole-genome alignments. Instead of searching for differences, SyRI starts by finding all co-linear regions between the genomes. As all remaining regions are SRs by definition, they just have to be classified as inversions, translocations, or duplications based on their positions in convoluted networks of repetitive alignments. Finally, SyRI reports local variations like SNPs and indels within syntenic and rearranged regions. We show SyRIs broad applicability to multiple species and genetically validate the presence of ~100 translocations identified in Arabidopsis.