Workflow of GeneMiner
GeneMiner is a Python-based tool used to mine phylogenetic markers from NGS data. It consists of three major steps (Figure 2 A-C). First, it collects reads that reliably map to the reference of closely related taxa using a k-mer filtering method. Next, it uses a hybrid assembly algorithm, a reference-guided de Bruijn graph assembly with seed self-discovery and a greedy extension method, to recover the target genes. Finally, it employs a mutation model and repeated resampling to statistically evaluate the impact of the reference on the assembly and confirm the assembly results.