Using information about pairwise chromatin connections between assembled sequences, this tool constructs a graph and allows interconnected groups of sequences to be clustered, labelled and visualised. Distinct genomes from contaminated samples can therefore be separated, even when reference-based taxonomic assignment is difficult. The procedure is based on the node2vec algorithm.
Selectively display chromatin contact maps based on a list of contigs or scaffolds of interest, using a cooler file as input. Useful for displaying small fragments, or clusters identified by node2vec.
If you use code from this repository, please cite: Kudoa genomes from contaminated hosts reveal extensive gene order conservation and rapid sequence evolution https://www.biorxiv.org/content/10.1101/2024.11.01.621499v1