Manticore addresses the subgenomic intermixing state of a hybrid, allopolyploid genome. The user provides a reference FASTA file for the hybrid species and short illumina reads from its two parental species. Manticore studies the coverage profiles obtained from each parent and extracts a series of metrics in intervals of adjustable size, which define how intermixed the subgenomes are and where to find intermixed regions on the genome.
Manticore should be seen as a screening tool to extract intermixed regions for downstream targeted analyses.
Citation: Schiavinato et al., 2021
GitHub repository: link