An Efficient Means for Calling Moderate to Long Structural Variations (Korani)

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An Efficient Means for Calling Moderate to Long Structural Variations Through Pairwise Genomic Comparison And Kmers
Walid Korani, Hudson Alpha Institute for Biotechnology
2021 APRES Annual Meeting - Breeding, Genetics & Biotechnology I

Although structure variations are less abundant than SNPs, they control many economical traits in different species. Calling valid structural variations is a computationally expensive and timeconsuming process. We developed a computational approach, designated Cyclops, to compare two genomes and extract moderate to long insertions and deletions utilizing high multiple threading, which allows running each chromosomal pair in a thread in pairwise comparison of all chromosomes from the two genomes. A second round of runs is implemented to extract high quality structure variances by using Kmers extracted from Deletions/Insertions and aligned to the opposite genome, then re-stacked based on the hit results. In a case study using a novel assembled NC94022 genome against the Tifrunner genome, Cyclops recognized 309,186 deletions and 17,009 insertions, varied from 40 bp to 39 kbp in less than three hours.
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Management
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