SyRI

SyRI identifies genomic rearrangements and local sequence differences between pairwise whole-genome assemblies at the chromosome level to characterize inversions, translocations, duplications, SNPs, and indels.

Key Features:

• Pairwise whole-genome comparison: Performs pairwise whole-genome comparisons at the chromosome level.
• Rearrangement detection: Identifies rearranged regions including inversions, translocations, and duplications.
• Local sequence-difference discovery: Searches for sequence differences within rearranged regions.
• Syntenic distinction: Distinguishes sequences in syntenic (conserved) regions from those in rearranged regions.
• Variant annotation: Annotates single nucleotide polymorphisms (SNPs), insertions and deletions (indels), and complex structural changes.
• Resolution of similar sequences: Resolves highly similar sequences that differ in genomic location, orientation, or copy number.

Scientific Applications:

• Comparative genomics and evolution: Characterizing structural variation and sequence divergence for evolutionary analyses.
• Disease genomics: Identifying structural variants and local sequence differences relevant to disease research.
• Population genetics and genetic diversity: Annotating genetic diversity and variant inheritance patterns within and between genomes.

Methodology:

Performs pairwise chromosome-level whole-genome comparisons, identifies rearranged regions (e.g., inversions, translocations, duplications), searches for sequence differences within those regions, distinguishes syntenic versus rearranged regions, and annotates SNPs, indels, and complex structural changes.