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

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, translocation...

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Bibliographic Details
Published in:Genome Biology 2019-12, Vol.20 (1), p.277-277, Article 277
Main Authors: Goel, Manish, Sun, Hequan, Jiao, Wen-Biao, Schneeberger, Korbinian
Format: Article
Language:English
Subjects:
Animals
Arabidopsis
Chromosome translocations
Chromosomes
Copy number
Gene Rearrangement
Genetic Techniques
Genetics
Genome alignments
Genome comparison
Genomes
Genomics - methods
Humans
Identification
Nucleotide sequence
Single-nucleotide polymorphism
Software
Structural rearrangements
Structural variations
Synteny
Variant calling
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Summary: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.
ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-019-1911-0