mode metaextrachromosomal
two_step_rr false

simp
{

    ; suspecies bulge remover:
    subspecies_br
    {
        enabled true
        main_iteration_only true
        max_bulge_length_coefficient    30.     ; max_bulge_length = max_bulge_length_coefficient * k
        max_coverage            1000000.0
        max_relative_coverage       15     ; bulge_cov < this * not_bulge_cov
        max_delta 45
        max_relative_delta 0.2
        min_identity 0.7
    }

}
plasmid
{
;isolated
    long_edge_length 1000
    edge_length_for_median 10000
    relative_coverage 0.3
    small_component_size 10000
    small_component_relative_coverage 1.5
    min_component_length 10000
    min_isolated_length 1000
;   reference_removal replace this with path to reference and uncomment for reference based filtration
;meta                          
    iterative_coverage_elimination true
    additive_step 5
    relative_step 1.3
    max_length 1000000
    output_linear true
    min_circular_length 1000
    min_linear_length 500
}
