config.yaml

pathracer:
  evalue: 0.000000001
  min_length: 0.9
  max_size: 2500000

orfs_search:
  max_restorable_length: 3000  # maximum distance in the graph from alignment where start/stodon can be found
  max_path_length: 1500        # maximum length of path to start/stop codon
  min_path_length: 0           # minimum length of path to start/stop codon
  max_paths_num: 2000          # maximum number of paths can be generated during reconstruction of paths to start/stop codons
  min_unique_edge_length: 500  # length of edges that considered us unique during filtering based on contigs

orfs_filtering:
  min_reliable_length: 100     # second minimum length of edge for filtering (used only if there is no edges with length > reliable length)
  reliable_length: 300         # minimum length of edge for filtering
  identity: 90                 # single-linkage clustering cluster two sequence into the same cluster if they are similar > indetity
  ed_threshold: 0.2            # threshold for edit distance calculation