Description

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.

Use case

Manticore should be seen as a screening tool to extract intermixed regions for downstream targeted analyses.

Useful links

Citation: Schiavinato et al., 2021

GitHub repository: link