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.