bioa.algorithms.reconstruction.amplicon_frequency_matrix_strategy_from_graph

amplicon_frequency_matrix_strategy_from_graph(graph, use_chi_sqrd=False)

Reconstructs quasispecies from the supplied graph.

An amplicon strategy is used to pair reads with one another using a most consistent function.

Parameters :

graph : DecliquedAmpliconReadGraph

Amplicon read graph with fork vertices added.

use_chi_sqrd : bool (optional, default=False)

Whether to use the chi squared test in selecting a guide or the uniform distribution.

Returns :

quasispecies : dict

Quasispecies spectrum with sequences as keys and frequency as value.