Conclusion
In summary, GeneMiner is a convenient and efficient tool that utilizes a reference-guided de Bruijn graph with seed self-discovery and a greedy extension for phylogenetic marker extraction from non-model organisms using NGS data. GeneMiner offers a highly optimized approach for validating assembly results through a range of optimization techniques. With outstanding speed and optimal resource utilization, GeneMiner supports multi-core parallel computing and allows for limited memory consumption. It can easily be used on both high-performance computing clusters and standard personal computers. GeneMiner is open-source, easy to install, user-friendly, and compatible with all widely used operating systems (i.e., Linux, Windows, and macOS). Overall, this software fills a need in the field for easy-to-use tools for mining NGS data from non-model organisms.