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).

本数据集提供两款Bash脚本，可基于扩增子测序（amplicon sequencing，SSRseq、SSR-GBS或Lepais等人2019年发表的文献[https://doi.org/10.7717/peerj.9085]中描述的类似方法）生成的序列数据，实现自动化的基于序列的微卫星基因分型（microsatellite genotyping）。首款脚本用于对比不同分析策略与参数下生成的基因分型质量；第二款脚本则可通过优化后的参数生成最终的基因型数据集。此外还提供一款虚拟机（.ova格式文件），可将其导入至VirtualBox中，运行其中预装了所有工具（含本脚本、软件依赖项与示例文件）且可直接投入使用的Ubuntu系统。