## use just in time compilation for bbmap
usejni: false

gene_annotations: []

genome_filter_criteria: "(Completeness-5*Contamination >50 ) & (Length_scaffolds >=50000) & (Ambigious_bases <1e6) & (N50 > 5*1e3) & (N_scaffolds < 1e3)"
exclude_unplacable_genomes: false

genome_dereplication:
  ANI: 0.95 ## Genome dreplication threshold
  overlap: 0.2 # See more on https://drep.readthedocs.io/en/latest/module_descriptions.html
  greedy_clustering: "auto" # Add options for greedy clustering 'auto' when using more than 5k bins
  opt_parameters: ""
  score:
    completeness: 1
    contamination: 5
    N50: 0.5
    length: 0
    centrality: 1

genome_aligner: "minimap"

bin_quality_asesser: checkm2 #[ checkm2, busco, cehckm]

semibin_options: ""
semibin_train_extra: ""

filter_chimieric_bins: true
gunc_database: "progenomes" # progenomes or gtdb

binner: # If DASTool is used as final_binner, use predictions of this binners
  - metabat
  - maxbin
#  - vamb

cobinning_readmapping_id: 0.95 #when mapping different reads to contigs from different samples use less stringent alignment threshold

preprocess_qtrim: "rl"
preprocess_kmer_trim: "r"
preprocess_minimum_base_quality: 10
preprocess_allowable_kmer_mismatches: 1
preprocess_reference_kmer_match_length: 27
preprocess_minimum_passing_read_length: 51
preprocess_minimum_base_frequency: 0.05
preprocess_max_ns: -1
preallocate_ram: "t"
error_correction_overlapping_pairs: "t"
