Automated pipeline for sequence-based microsatellite genotyping

Two bash scripts are provided to automated sequence-base microsatellite genotyping from data sequences generated by amplicon sequencing (SSRseq, SSR-GBS or similar approaches as described in Lepais et al. 2019, https://doi.org/10.7717/peerj.9085). The first script is used to compare genotype quality generated using different analyses strategies and parameters. The second script is used to generate the final genotypic dataset using optimized parameters. A virtual machine (.ova file) can be import into VirtualBox to execute an Ubuntu system that includes all tools already installed and ready to use (including scripts, software dependencies and example files).