SV scripts By Lei Gao (lg397@cornell.edu; leigao@wbgcas.cn) Fei lab (http://bioinfo.bti.cornell.edu/) Version 1.1 Date: 08/27/2020 This pipeline is designed to (1) detect structural variants (SVs) between high-quality genomes of two closely related species/varieties and (2) genotype the SVs in a population based on resequencing data.

SV detection scripts: SV_calling SV genotyping scripts: SV_genotyping

Citation: Wang X, Gao L, Jiao C, Stravoravdis S, Hosmani P, Saha S, Zhang J, Mainiero S, Strickler S, Catala C, Martin G, Mueller L, Vrebalov J, Giovannoni J, Wu S, Fei Z: Genome of Solanum pimpinellifolium provides insights into structural variants during tomato breeding. bioRxiv 2020: https://doi.org/10.1101/2020.06.17.157859