Structural variation data from a Dutch European flat oyster (Ostrea edulis) population

This repository contains structural variant (SV) and single nucleotide polymorphism (SNP) call sets generated de novo from whole-genome Nanopore sequencing data for 35 individuals of Ostrea edulis sampled from Lake Grevelingen, the Netherlands. All variants were called using the xbOstEdul1.1 reference genome (NCBI RefSeq Assembly: GCF_947568905.1).
Structural variants were called using three tools: SVIM, cuteSV, and Sniffles2. Only SVs identified by all three tools were retained. SNPs were called using Clair3.
During SV analysis, several variants appeared to correspond to repeat sequences. A FASTA file containing the corresponding consensus sequences (generated using CD-HIT and seqtk) is also provided in this repository.