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

ABSTRACT: Genomic differences range from single nucleotide differences to complex structural variations. Current methods typically annotate sequence differences ranging from SNPs to large indels accurately but do not unravel the full complexity of structural rearrangements, including inversions, translocations, and duplications, where highly similar sequence changes in location, orientation, or copy number. Here, we present SyRI, a pairwise whole-genome comparison tool for chromosome-level assemblies. SyRI starts by finding rearranged regions and then searches for differences in the sequences, which are distinguished for residing in syntenic or rearranged regions. This distinction is important as rearranged regions are inherited differently compared to syntenic regions.

SUBMITTER: Goel M

PROVIDER: S-EPMC6913012 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature

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

Goel Manish M Sun Hequan H Jiao Wen-Biao WB Schneeberger Korbinian K

Genome biology 20191216 1

Genomic differences range from single nucleotide differences to complex structural variations. Current methods typically annotate sequence differences ranging from SNPs to large indels accurately but do not unravel the full complexity of structural rearrangements, including inversions, translocations, and duplications, where highly similar sequence changes in location, orientation, or copy number. Here, we present SyRI, a pairwise whole-genome comparison tool for chromosome-level assemblies. SyR ...[more]

PMID: 31842948

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