<i>SaVor</i> - A Reproducible Structural Variant Calling and Benchmarking Platform from Short-Read Data.

ABSTRACT: Structural variations (SVs) are differences in genomic regions that are larger than 1 kilobase-pair (Kbp) between individuals, and can arise from errant DNA repair mechanisms, whole genome duplications, and transposable element activity across the genome. Recent advances, optimizations, and cost reductions in next generation sequencing technologies have facilitated the exponential increase in the amount of available short read genomic data. Here we present SaVor, a flexible, reproducible SV calling workflow that accepts single or multi-lane short-read paired-end Illumina sequence data, or BAM files as input to generate a consensus SV call-set based on user-provided merge parameters. We tested SaVor on 1,165 Arabidopsis thaliana whole genome sequences and benchmarked it

SUBMITTER: Mugoya T 

PROVIDER: S-EPMC12687769 | biostudies-literature | 2025 Dec

REPOSITORIES: biostudies-literature