mode    plasmid

plasmid 
{
;isolated
    long_edge_length 1000
    edge_length_for_median 10000
    relative_coverage 0.3
    small_component_size 10000
    small_component_relative_coverage 2
    min_component_length 10000
    min_isolated_length 1000
;meta
    meta_mode true
    remove_list ""
    absolute_coverage_cutoff 5
    circular_removal true
;circular_removal
    min_start_edge_length 2000
    min_start_coverage 20
    max_loop 150000
;   reference_removal replace this with path to reference and uncomment for reference based filtration
    HMM_filtration none ;"do","use" "none"
;iterative_coverage_elimination
    iterative_coverage_elimination true
    iterative_step 5
    max_length 1000000
}
